9yzs

Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence TAATTAGGCCG and loaded with Even-skipped homeodomain

Method: X-RAY DIFFRACTION D_max: 101.0 Å Quality: REASONABLE

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Replication initiation protein

Escherichia coli

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Heteromer Protein × 3 DNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain C； UniProt 1–251	Not recorded	DNA (31-MER) × 1 DNA (31-MER) × 1 Segmentation protein even-skipped × 2 （P06602） MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；30mM magnesium acetate, 800mM lithium sulfate, 50mM MES pH 6.5. The crystal was crosslinked with 47.5mg/mL EDC overnight, and then looped into a solution of 50mM potassium chloride, 4mM calcium chloride, 10% glycerol, and 10mM Tris hydrochloride for 1 hour. The drop was then supplemented with 30 micromolar Even-skipped homeodomain.	Resolution 3.08 Å R-free 0.291

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9YZS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1REP CRYSTAL STRUCTURE OF REPLICATION INITIATOR PROTEIN REPE54 OF MINI-F PLASMID COMPLEXED WITH AN ITERON DNA Deposited 1999-04-29	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Mutation：R118P	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；12 % PEG 400, 200 MM MGCL2, 100 MM TRIS-HCL, PH8.0, VAPOR DIFFUSION, HANGING DROP	Resolution 2.60 Å R-free 0.274
2Z9O Crystal structure of the dimeric form of RepE in complex with the repE operator DNA Deposited 2007-09-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–251（250 aa） Chain B 2–251（250 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；277 K；10% PEG 4000, 200mM Sodium Chloride, 5mM Samarium Chloride, 100mM HEPES-NaOH, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.14 Å R-free 0.313
7RVA Updated Crystal Structure of Replication Initiator Protein REPE54. Deposited 2021-08-18	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Mutation：R118P	NA SODIUM ION × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；300 mM MgCl2, 18% PEG 400, and 100 mM Tris HCl	Resolution 1.89 Å R-free 0.249
7U6K Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence. Deposited 2022-03-04	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Mutation：R118P	MG MAGNESIUM ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；400 mM MgCl2, 24% PEG 400, and 80 mM Tris HCl	Resolution 2.38 Å R-free 0.224
7U7O Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional T-A rich sequence. Deposited 2022-03-07	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Mutation：R118P	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；300 mM MgCl2, 28% PEG 400, and 80 mM Tris HCl	Resolution 2.97 Å R-free 0.258
7UFX Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and scaffold-insert duplexes (21mer and 10mer) containing the cognate REPE54 sequence and an additional G-C rich sequence, respectively. Deposited 2022-03-23	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric	Chain C 1–251（251 aa）	Mutation：R118P	MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；180 mM MgCl2, 20% PEG 400, and 100 mM Tris HCl	Resolution 2.80 Å R-free 0.226
7UOG Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and asymmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence. Deposited 2022-04-12	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Mutation：R118P	MG MAGNESIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；200 mM MgCl2, 30% PEG 400, and 100 mM Tris HCl	Resolution 2.63 Å R-free 0.221
7UR0 Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and scaffold-insert duplexes (21mer and 10mer) containing the cognate REPE54 sequence and an additional T-A rich sequence, respectively. Deposited 2022-04-20	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric	Chain C 1–251（251 aa）	Mutation：R118P	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；120 mM MgCl2, 20% PEG 400, 100 mM Tris HCl pH 8.0	Resolution 3.30 Å R-free 0.275
7UV6 Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and scaffold duplex (21mer) containing the cognate REPE54 sequence and an insert duplex (10mer) with guest TAMRA-labelled thymine and G-C rich sequence. Deposited 2022-04-29	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric	Chain C 1–251（251 aa）	Mutation：R118P	MG MAGNESIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；300 mM MgCl2, 15% PEG 400, and 100 mM Tris HCl	Resolution 2.72 Å R-free 0.224
7UV7 Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and scaffold duplex (21mer) containing the cognate REPE54 sequence and an insert duplex (10mer) with guest TAMRA-labelled thymine and T-A rich sequence. Deposited 2022-04-29	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric	Chain C 1–251（251 aa）	Mutation：R118P	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；200 mM MgCl2, 30% PEG 400, 100 mM Tris HCl pH 8.0	Resolution 3.02 Å R-free 0.269
7UXY Isoreticular, interpenetrating co-crystal of protein variant Replication Initiator Protein REPE54 (L53G,Q54G,E55G) and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence. Deposited 2022-05-06	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Mutation：R118P,L53G,Q54G,E55G	MG MAGNESIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；350 mM MgCl2, 30% PEG 400, and 100 mM Tris HCl	Resolution 3.15 Å R-free 0.264
8AAN The nucleoprotein complex of Rep protein with iteron containing dsDNA and DUE ssDNA. Deposited 2022-07-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 1–251（251 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；10% w/v PEG 20 000, 20% v/v PEG MME 550 0.02M of each carboxylic acid (0.2 M sodium formate, 0.2M ammonium acetate, 0.2M trisodium citrate, 0.2M sodium potassium L-tartrate, 0.2M sodium oxamate), 0.1M MES/imidazole pH 6.5.	Resolution 2.19 Å R-free 0.233
8AC8 The nucleoprotein complex of Rep protein with DUE ssDNA Deposited 2022-07-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain C 1–251（251 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；PEG 8000, ethylene glycol, HEPES, halogens	Resolution 1.60 Å R-free 0.243
8AC8 The nucleoprotein complex of Rep protein with DUE ssDNA Deposited 2022-07-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–251（251 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；PEG 8000, ethylene glycol, HEPES, halogens	Resolution 1.60 Å R-free 0.243
8D86 Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence co-crystallized with a guest small molecule, netropsin. Deposited 2022-06-07	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Mutation：R118P	MG MAGNESIUM ION × 5 NT NETROPSIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；300 mM MgCl2, 25% PEG 400, and 100 mM Tris HCl	Resolution 3.12 Å R-free 0.234
8D8M Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence grown in a calcium chloride crystallization solution. Deposited 2022-06-08	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Mutation：R118P	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；400 mM MgCl2, 24% PEG 400, and 80 mM Tris HCl	Resolution 3.10 Å R-free 0.255
8TIP Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence with blunt ends and 5' terminal phosphates. Deposited 2023-07-20	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Mutation：R118P	MG MAGNESIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；400 mM MgCl2, 25% PEG 400, and 100 mM Tris HCl	Resolution 2.79 Å R-free 0.240
8TIQ Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence with blunt ends and 3' terminal phosphates. Deposited 2023-07-20	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Mutation：R118P	MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；350 mM MgCl2, 25% PEG 400, and 100 mM Tris HCl	Resolution 2.45 Å R-free 0.267
8TIR Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence with 1 sticky bases and 5' terminal phosphates. Deposited 2023-07-20	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Mutation：R118P	MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；350 mM MgCl2, 30% PEG 400, and 100 mM Tris HCl	Resolution 3.11 Å R-free 0.242
8TIS Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence with 1 sticky bases and 3' terminal phosphates. Deposited 2023-07-20	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Mutation：R118P	MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；350 mM MgCl2, 25% PEG 400, and 100 mM Tris HCl	Resolution 2.54 Å R-free 0.278
8TIT Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence with 2 sticky base overhangs and no terminal phosphates. Deposited 2023-07-20	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Mutation：R118P	MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；450 mM MgCl2, 25% PEG 400, and 100 mM Tris HCl	Resolution 2.84 Å R-free 0.240
8TIU Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence with 2 sticky base overhangs and 3' terminal phosphates. Deposited 2023-07-20	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Mutation：R118P	MG MAGNESIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；400 mM MgCl2, 30% PEG 400, and 100 mM Tris HCl	Resolution 3.90 Å R-free 0.231
8TIV Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence with blunt ends and 5' terminal phosphates and crosslinked with EDC. Deposited 2023-07-20	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Mutation：R118P	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；350 mM MgCl2, 25% PEG 400, and 100 mM Tris HCl	Resolution 3.35 Å R-free 0.260
8TIW Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence with blunt ends and 3' terminal phosphates and crosslinked with EDC. Deposited 2023-07-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；350 mM MgCl2, 25% PEG 400, and 100 mM Tris HCl	Resolution 3.11 Å R-free 0.212
8TIX Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence with 1 sticky bases and 5' terminal phosphates and crosslinked with EDC. Deposited 2023-07-20	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Mutation：R118P	MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；350 mM MgCl2, 30% PEG 400, and 100 mM Tris HCl	Resolution 2.91 Å R-free 0.228
8TIY Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence with 1 sticky bases and 3' terminal phosphates and crosslinked with EDC. Deposited 2023-07-20	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Mutation：R118P	MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；350 mM MgCl2, 25% PEG 400, and 100 mM Tris HCl	Resolution 3.11 Å R-free 0.231
8TIZ Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence with 2 sticky base overhangs and no terminal phosphates and crosslinked with EDC. Deposited 2023-07-20	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Mutation：R118P	MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；450 mM MgCl2, 25% PEG 400, and 100 mM Tris HCl	Resolution 3.11 Å R-free 0.217
8TJ0 Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence with 2 sticky base overhangs and 5' terminal phosphates and crosslinked with EDC. Deposited 2023-07-20	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Mutation：R118P	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；400 mM MgCl2, 24% PEG 400, and 80 mM Tris HCl	Resolution 3.24 Å R-free 0.225
8TJ1 Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence with 2 sticky base overhangs and 3' terminal phosphates and crosslinked with EDC. Deposited 2023-07-20	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Mutation：R118P	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；400 mM MgCl2, 30% PEG 400, and 100 mM Tris HCl	Resolution 3.15 Å R-free 0.225
9NB0 Isoreticular, Porous co-crystal of Replication Initiator Protein REPE54 and asymmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and additional expansion sequence Deposited 2025-02-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；500mM Lithium Sulfate, 20mM Magnesium Acetate, 50mM MES	Resolution 3.20 Å R-free 0.197
9NCR Isoreticular, Porous co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and additional G/C rich expansion sequence Deposited 2025-02-17	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；1M lithium sulfate, 30mM Magnesium acetate, 50mM MES	Resolution 3.24 Å R-free 0.231
9YZA Isoreticular co-crystal 1 of protein variant Replication Initiator Protein REPE54 (L53G, Q54G, E55G) with symmetrical expanded duplex (31mer) containing insert sequence CCCGGCCGGA Deposited 2025-10-30	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Mutation：L53G, Q54G, E55G	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；10 mM Magnesium acetate, 1300 mM Lithium sulfate, 50 mM MES pH 6.5	Resolution 3.05 Å R-free 0.309
9YZB Isoreticular co-crystal 1 with symmetrical expanded duplex (31mer) containing insert sequence ACGGTAATTA Deposited 2025-10-30	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；10 mM Magnesium acetate, 1.6M Lithium sulfate, 50 mM MES pH 6.5	Resolution 4.13 Å R-free 0.253
9YZC Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence CGCGCGCGCG Deposited 2025-10-30	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Not recorded	MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；80 mM Magnesium acetate, 1.2 M Lithium sulfate, 50 mM MES pH 6.5	Resolution 3.16 Å R-free 0.299
9YZD Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence CTAATTAGGC Deposited 2025-10-30	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；30 mM Magnesium acetate, 1.3 M Lithium sulfate, 50 mM MES pH 6.5	Resolution 3.09 Å R-free 0.265
9YZE Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence TGATGAGCAG Deposited 2025-10-30	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；20 mM Magnesium acetate, 300 mM Lithium sulfate, 50 mM MES pH 6.5	Resolution 4.07 Å R-free 0.276
9YZF Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence AATTAGGCCG Deposited 2025-10-30	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；50 mM Magnesium acetate, 1.1 M Lithium sulfate, 50 mM MES pH 6.5	Resolution 3.07 Å R-free 0.241
9YZG Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence ATGAGTCATA Deposited 2025-10-30	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；20 mM Magnesium acetate, 1.4 M Lithium sulfate, 50 mM MES pH 6.5	Resolution 3.09 Å R-free 0.301
9YZI Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence CCCGGCCGGA Deposited 2025-10-30	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Not recorded	MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；50 mM Magnesium acetate, 1.6 M Lithium sulfate, 50 mM MES pH 6.5	Resolution 4.00 Å R-free 0.322
9YZJ Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence CGTAATTAGG Deposited 2025-10-30	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Not recorded	MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；30 mM Magnesium acetate, 1.7 M Lithium sulfate, 50 mM MES pH 6.5	Resolution 2.97 Å R-free 0.292
9YZK Isoreticular co-crystal 1 with symmetrical expanded duplex (42mer) containing insert sequence ACCCTTCTATGACCTACTCCA Deposited 2025-10-30	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；60mM Magnesium acetate, 1.6M Lithium sulfate, 50mM MES pH 6.5	Resolution 5.10 Å R-free 0.304
9YZL Isoreticular co-crystal of Replication Initiator Protein REPE54 and asymmetrical expanded duplex (31mer) containing the cognate REPE54 sequence, and additional T-A rich sequence with 5' terminal phosphates. Two copies of Even-skipped homeodomain loaded post-crystallization Deposited 2025-10-30	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain C 1–251（251 aa）	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；30mM Magnesium Acetate, 1.2M Lithium sulfate, 50mM MES pH 6.5. The crystal was crosslinked with 33mg/mL EDC overnight, and then looped into a solution of 15mM potassium chloride, 4mM calcium chloride, 10% glycerol, and 10mM Tris hydrochloride for 1 hour. The drop was then supplemented with 30 micromolar Even-skipped homeodomain	Resolution 3.02 Å R-free 0.294
9YZM Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence CTAATTAGGC and loaded with Even-skipped homeodomain Deposited 2025-10-30	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain C 1–251（251 aa）	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；30mM magnesium acetate, 1.1M lithium sulfate, 50mM MES pH 6.5. The crystal was crosslinked with 33mg/mL EDC overnight, and then looped into a solution of 50mM potassium chloride, 4mM calcium chloride, 10% glycerol, and 10mM Tris hydrochloride for 1 hour. The drop was then supplemented with 30 micromolar Even-skipped homeodomain.	Resolution 3.07 Å R-free 0.269
9YZN Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence TGATGAGCAG and loaded with Even-skipped homeodomain Deposited 2025-10-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain C 1–251（251 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；40mM Magnesium acetate, 1.4M Lithium sulfate, 50mM MES pH 6.5. The crystal was crosslinked with 33mg/mL EDC overnight, and then looped into a solution of 25mM potassium chloride, 4mM calcium chloride, 10% glycerol, and 10mM Tris hydrochloride for 1 hour. The drop was then supplemented with 30 micromolar Even-skipped homeodomain.	Resolution 3.16 Å R-free 0.283
9YZO Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence TGATGAGCAG and loaded with Even-skipped homeodomain Deposited 2025-10-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain C 1–251（251 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；20mM magnesium acetate, 1.7M lithium sulfate, 50mM MES pH 6.5. The crystal was crosslinked with 33mg/mL EDC overnight, and then looped into a solution of 50mM potassium chloride, 4mM calcium chloride, 10% glycerol, and 10mM Tris hydrochloride for 1 hour. The drop was then supplemented with 30 micromolar Even-skipped homeodomain.	Resolution 2.96 Å R-free 0.312
9YZP Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence TGATGAGCAG and loaded with ultrabithorax homeodomain Deposited 2025-10-30	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain C 1–251（251 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；40mM Magnesium acetate, 1.5M Lithium sulfate, 50mM MES pH 6.5. The crystal was crosslinked with 45mg/mL EDC overnight, and then looped into a solution of 50mM potassium chloride, 4mM calcium chloride, 10% glycerol, and 10mM Tris hydrochloride for 1 hour. The drop was then supplemented with 40 micromolar Ultrabithorax homeodomain.	Resolution 3.67 Å R-free 0.295
9YZQ Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence TGATGAGCAG and loaded with Engrailed homeodomain enhanced Green fluorescent protein fusion Deposited 2025-10-30	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: tetrameric	Chain C 1–251（251 aa）	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；40mM Magnesium acetate, 1.4M Lithium sulfate, 50mM MES pH 6.5. The crystal was crosslinked with 45mg/mL EDC overnight, and then looped into a solution of 50mM potassium chloride, 4mM calcium chloride, 10% glycerol, and 10mM Tris hydrochloride for 1 hour. The drop was then supplemented with 22 micromolar engrailed homeodomain-enhanced Green fluorescent protein fusion	Resolution 3.75 Å R-free 0.338
9YZR Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence TAATTAGGCCG and loaded with ultrabithorax homeodomain Deposited 2025-10-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain C 1–251（251 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；30mM magnesium acetate, 900mM Lithium sulfate, 50mM MES pH 6.5. The crystal was crosslinked with 48mg/mL EDC overnight, and then looped into a solution of 35mM potassium chloride, 4mM calcium chloride, 10% glycerol, and 10mM Tris hydrochloride for 1 hour. The drop was then supplemented with 80 micromolar Ultrabithorax homeodomain.	Resolution 3.39 Å R-free 0.298
9YZT Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence TAATTAGGCCG and loaded with Antennapedia homeodomain Deposited 2025-10-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain C 1–251（251 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；30mM Magnesium acetate, 1.1M Lithium sulfate, 50mM MES pH 6.5. The crystal was crosslinked with 47.5mg/mL EDC overnight, and then looped into a solution of 50mM potassium chloride, 4mM calcium chloride, 10% glycerol, and 10mM Tris hydrochloride for 1 hour. The drop was then supplemented with 23 micromolar Even-skipped homeodomain.	Resolution 3.30 Å R-free 0.292
9YZU Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence ATGAGTCATA and loaded with mutated Bzip region of GCN4 transcription factor Deposited 2025-10-30	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain C 1–251（251 aa）	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；50mM magnesium acetate, 1.8M lithium sulfate, 50mM MES pH 6.5. The crystal was crosslinked with 50mg/mL EDC overnight, and then looped into a solution of 50mM potassium chloride, 4mM calcium chloride, 10% glycerol, and 10mM Tris hydrochloride for 1 hour. The drop was then supplemented with 33 micromolar bZip	Resolution 3.05 Å R-free 0.246
9Z08 Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing separate insert strand with sequence GACGGTAATT Deposited 2025-10-31	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric	Chain C 1–251（251 aa）	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；10 mM Magnesium acetate, 1.3 M Lithium sulfate, 50 mM sodium cacodylate pH 6.5	Resolution 4.22 Å R-free 0.254
9Z1A Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence CCGCGCAGGC Deposited 2025-11-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；80 mM Magnesium Acetate, 1.2 M Lithium Sulfate, 50 mM MES pH 6.5	Resolution 3.10 Å R-free 0.335
9Z1B Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence CCGCGCAGGC, crystal soaked in alternate solvent prior to diffraction Deposited 2025-11-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Not recorded	CA CALCIUM ION × 2 K POTASSIUM ION × 3 MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；50mM Magnesium acetate, 1.6M Lithium sulfate, 50mM MES pH 6.5. The crystal was crosslinked with 40 mg/mL EDC overnight, and then looped into a solution of 50mM potassium chloride, 4mM calcium chloride, 10% glycerol, and 10mM Tris hydrochloride.	Resolution 3.88 Å R-free 0.308
9Z1C Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence CTAATTAGGC, crystal soaked in alternate solvent prior to diffraction Deposited 2025-11-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Not recorded	K POTASSIUM ION × 3 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；50mM Magnesium acetate, 1.5M Lithium sulfate, 50mM MES pH 6.5. The crystal was crosslinked with 33mg/mL EDC overnight, and then looped into a solution of 50mM potassium chloride, 4mM calcium chloride, 10% glycerol, and 10mM Tris hydrochloride.	Resolution 3.04 Å R-free 0.325
9Z1D Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence GCTTGATGAG, crystal soaked in alternate solvent prior to diffraction Deposited 2025-11-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；25mM Magnesium acetate, 800mM Lithium sulfate, 50mM MES pH 6.5. The crystal was crosslinked with 50mg/mL EDC overnight, and then looped into a solution of 10mM HEPES pH 6.5, 50mM sodium chloride, 2.5 mM magnesium chloride, 800mM lithium sulfate, 15mM magnesium acetate, 25mM MES pH 6.5, and 80 micromolar Ultrabithorax homeodomain.	Resolution 3.06 Å R-free 0.318
9Z44 Isoreticular co-crystal 1 with symmetrical expanded duplex (31mer) containing insert sequence CCCGGCCGGA and loaded with C-clamp domain Deposited 2025-11-08	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain C 1–251（251 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；60mM magnesium acetate, 1.8M lithium sulfate, 50mM MES pH 6.5.The crystal was crosslinked with 50 mg/mL EDC overnight, and then looped into a solution of 50mM potassium chloride, 4mM calcium chloride, 10% glycerol, and 10mM Tris hydrochloride for 1 hour. The drop was then supplemented with 90 micromolar C-clamp	Resolution 7.20 Å R-free 0.345
9Z4E Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence CATGAGTCAT and loaded with mutated Bzip region of GCN4 transcription factor Deposited 2025-11-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain C 1–251（251 aa）	Not recorded	MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；50mM magnesium acetate, 1.6M Lithium sulfate, 50mM MES pH 6.5. The crystal was crosslinked with 47.5 mg/mL EDC overnight, and then looped into a solution of 50mM potassium chloride, 4mM calcium chloride, 10% glycerol, and 10mM Tris hydrochloride for 1 hour. The drop was then supplemented with 100 micromolar bZip	Resolution 3.63 Å R-free 0.285
9Z55 Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence CATGAGTCAT Deposited 2025-11-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–251（251 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；40mM magnesium acetate, 1.8M lithium sulfate, 50mM MES pH 6.5	Resolution 3.94 Å R-free 0.316

57 other PDB entries and 58 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	REPE1_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 13–263； UniProt 1–251

Segmentation protein even-skipped

Drosophila melanogaster

UniProt P06602

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Heteromer Protein × 3 DNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain D； UniProt 69–129 Chain E； UniProt 69–129	Fragment：Even-skipped homeodomain	DNA (31-MER) × 1 DNA (31-MER) × 1 Replication initiation protein × 1 （P03856） MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；30mM magnesium acetate, 800mM lithium sulfate, 50mM MES pH 6.5. The crystal was crosslinked with 47.5mg/mL EDC overnight, and then looped into a solution of 50mM potassium chloride, 4mM calcium chloride, 10% glycerol, and 10mM Tris hydrochloride for 1 hour. The drop was then supplemented with 30 micromolar Even-skipped homeodomain.	Resolution 3.08 Å R-free 0.291

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9YZS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1JGG Even-skipped Homeodomain Complexed to AT-rich DNA Deposited 2001-06-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 70–129（60 aa） Fragment：Homeodomain Chain B 70–129（60 aa） Fragment：Homeodomain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；sodium acetate, potassium chloride, DTT, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.316
9YZL Isoreticular co-crystal of Replication Initiator Protein REPE54 and asymmetrical expanded duplex (31mer) containing the cognate REPE54 sequence, and additional T-A rich sequence with 5' terminal phosphates. Two copies of Even-skipped homeodomain loaded post-crystallization Deposited 2025-10-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain D 69–129（61 aa） Chain E 69–129（61 aa）	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；30mM Magnesium Acetate, 1.2M Lithium sulfate, 50mM MES pH 6.5. The crystal was crosslinked with 33mg/mL EDC overnight, and then looped into a solution of 15mM potassium chloride, 4mM calcium chloride, 10% glycerol, and 10mM Tris hydrochloride for 1 hour. The drop was then supplemented with 30 micromolar Even-skipped homeodomain	Resolution 3.02 Å R-free 0.294
9YZM Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence CTAATTAGGC and loaded with Even-skipped homeodomain Deposited 2025-10-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain D 69–129（61 aa） Chain E 69–129（61 aa）	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；30mM magnesium acetate, 1.1M lithium sulfate, 50mM MES pH 6.5. The crystal was crosslinked with 33mg/mL EDC overnight, and then looped into a solution of 50mM potassium chloride, 4mM calcium chloride, 10% glycerol, and 10mM Tris hydrochloride for 1 hour. The drop was then supplemented with 30 micromolar Even-skipped homeodomain.	Resolution 3.07 Å R-free 0.269
9YZN Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence TGATGAGCAG and loaded with Even-skipped homeodomain Deposited 2025-10-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain D 69–129（61 aa） Chain E 69–129（61 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；40mM Magnesium acetate, 1.4M Lithium sulfate, 50mM MES pH 6.5. The crystal was crosslinked with 33mg/mL EDC overnight, and then looped into a solution of 25mM potassium chloride, 4mM calcium chloride, 10% glycerol, and 10mM Tris hydrochloride for 1 hour. The drop was then supplemented with 30 micromolar Even-skipped homeodomain.	Resolution 3.16 Å R-free 0.283
9YZO Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence TGATGAGCAG and loaded with Even-skipped homeodomain Deposited 2025-10-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain D 69–129（61 aa） Chain E 69–129（61 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；20mM magnesium acetate, 1.7M lithium sulfate, 50mM MES pH 6.5. The crystal was crosslinked with 33mg/mL EDC overnight, and then looped into a solution of 50mM potassium chloride, 4mM calcium chloride, 10% glycerol, and 10mM Tris hydrochloride for 1 hour. The drop was then supplemented with 30 micromolar Even-skipped homeodomain.	Resolution 2.96 Å R-free 0.312

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	EVE_DROME
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 4–64； UniProt 69–129 Author chain E； PDBConstruct 4–64； UniProt 69–129

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9yzs
Deposition date deposition_date	2025-10-30
最后修订 last_revision	2026-02-18
Structure title title	Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence TAATTAGGCCG and loaded with Even-skipped homeodomain
Keywords keywords	Protein-DNA complex, DNA Binding protein, Transcription factor; DNA BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	28.97 Å
Radius of gyration Rg (electron density) rg_electron	27.99 Å
Forward intensity I(0) i0	74753700.00
Molecular weight molecular_weight	54820.0 kDa
Excluded volume excluded_volume	62871 Å³
Envelope volume envelope_volume	87334 Å³
Hydration-shell volume shell_volume	27743 Å³
Envelope diameter envelope_diameter	105.6 Å
Shell Rg shell_rg	32.92 Å
Envelope Rg envelope_rg	28.54 Å
Shape Rg shape_rg	27.93 Å
Total Rg total_rg	28.56 Å
Total atoms total_atoms	3789
Residues n_residues	390
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	101.0 Å
Rg (real space) rg_real	29.21 Å
Rg uncertainty (real space) rg_real_error	0.82 Å
I(0) (real space) i0_real	7.4750e+07
I(0) uncertainty (real space) i0_real_error	1.1030e+06
Rg (reciprocal space) rg_reciprocal	29.11 Å
I(0) (reciprocal space) i0_reciprocal	74750000.0000
Solution quality estimate total_estimate	0.6399
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	29.4 Å
Skewness Skewness skewness	0.576
Kurtosis Kurtosis kurtosis	-0.131
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6262000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.752; Stabil: 1.000; Sysdev: 0.156; Positv: 1.000; Valcen: 0.710; Smooth: 0.882

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	DNA (31-MER)
Molecular weight formula_weight	9472.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	A
Atom count atom_count	3809

CCTGTGACAAATTGCCCTCATAATTAGGCCG

Entity 2 Entity 2 polymer

Description description	DNA (31-MER)
Molecular weight formula_weight	9592.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

GCGGCCTAATTATGAGGGCAATTTGTCACAG

Entity 3 Entity 3 polymer

Description description	Replication initiation protein
Molecular weight formula_weight	30749.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MRGSHHHHHHGSMAETAVINHKKRKNSPRIVQSNDLTEAAYSLSRDQKRMLYLFVDQIRKSDGTLQEHDGICEIHVAKYAEIFGLTSAEASKDIRQALKSFAGKEVVFYRPEEDAGDEKGYESFPWFIKPAHSPSRGLYSVHINPYLIPFFIGLQNRFTQFRLSETKEITNPYAMRLYESLCQYRKPDGSGIVSLKIDWIIERYQLPQSYQRMPDFRRRFLQVCVNEINSRTPMRLSYIEKKKGRQTTHIVFSFRDITSMTTG

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 polymer

Description description	Segmentation protein even-skipped
Molecular weight formula_weight	7853.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E

GTGSVRRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQR

来源 Source

来源生物 organism	Drosophila melanogaster
通用名 common_name	fruit fly
NCBI Class编号 ncbi_taxonomy_id	7227
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

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8. Citations (2)

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Unit-cell length a length_a	74.193 Å
Unit-cell length b length_b	122.956 Å
Unit-cell length c length_c	135.180 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.86 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	I 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	monoclinic

Resolution resolution	3.080 Å
Low-resolution limit resolution_low	46.920 Å
R factor r_factor	0.2746
R_work r_work	0.2728
R_free r_free	0.2906

fit	/app/data/saxs_computation/yz/9yzs/9yzs.fit
pddf	/app/data/pr_computation/yz/9yzs/9yzs.pr.out
profile	/app/data/saxs_computation/yz/9yzs/9yzs.dat

Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence TAATTAGGCCG and loaded with Even-skipped homeodomain

1. Protein Identity and Related Structures Protein Identity & Related Structures

Replication initiation protein

State in the Current Structure

Other States of the Same Protein in the Database

Segmentation protein even-skipped

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 non-polymer

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)