9yzt

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

Method: X-RAY DIFFRACTION D_max: 99.8 Å Quality: GOOD

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1. 蛋白身份与相关结构 Protein Identity & Related Structures

Replication initiation protein

Escherichia coli

当前结构中的状态

Assembly	聚集状态	构建体	突变与修饰	配体、离子与共同组分	实验方法与环境	结构质量
1	蛋白–DNA 异源复合物蛋白 × 3 DNA 2 PDB 声明：pentameric（5）与全部聚合物数一致	链 C； UniProt 1–251	未记录	DNA (31-MER) × 1 DNA (31-MER) × 1 Homeotic protein antennapedia × 2 （P02833） MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件：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.	分辨率 3.30 Å R-free 0.292

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly， “相对当前条目”直接指出证据层面的不同；没有差异标签表示当前已读取字段一致。

其他 PDB	相对当前条目 9YZT	Assembly / 聚集状态	构建体	突变与修饰	配体、离子与非聚合物	实验方法与环境	结构质量
1REP CRYSTAL STRUCTURE OF REPLICATION INITIATOR PROTEIN REPE54 OF MINI-F PLASMID COMPLEXED WITH AN ITERON DNA 提交 1999-04-29	突变/修饰不同聚集状态不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	突变：R118P	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8；12 % PEG 400, 200 MM MGCL2, 100 MM TRIS-HCL, PH8.0, VAPOR DIFFUSION, HANGING DROP	分辨率 2.60 Å R-free 0.274
2Z9O Crystal structure of the dimeric form of RepE in complex with the repE operator DNA 提交 2007-09-21	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 同源多聚体；蛋白 × 2 PDB 声明：tetrameric	链 A 2–251（250 aa）链 B 2–251（250 aa）	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 3.14 Å R-free 0.313
7RVA Updated Crystal Structure of Replication Initiator Protein REPE54. 提交 2021-08-18	突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	突变：R118P	NA SODIUM ION × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；300 mM MgCl2, 18% PEG 400, and 100 mM Tris HCl	分辨率 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. 提交 2022-03-04	突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	突变：R118P	MG MAGNESIUM ION × 7	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；400 mM MgCl2, 24% PEG 400, and 80 mM Tris HCl	分辨率 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. 提交 2022-03-07	突变/修饰不同聚集状态不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	突变：R118P	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；300 mM MgCl2, 28% PEG 400, and 80 mM Tris HCl	分辨率 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. 提交 2022-03-23	突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：pentameric	链 C 1–251（251 aa）	突变：R118P	MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；180 mM MgCl2, 20% PEG 400, and 100 mM Tris HCl	分辨率 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. 提交 2022-04-12	突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	突变：R118P	MG MAGNESIUM ION × 5	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；200 mM MgCl2, 30% PEG 400, and 100 mM Tris HCl	分辨率 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. 提交 2022-04-20	突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：pentameric	链 C 1–251（251 aa）	突变：R118P	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；120 mM MgCl2, 20% PEG 400, 100 mM Tris HCl pH 8.0	分辨率 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. 提交 2022-04-29	突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：pentameric	链 C 1–251（251 aa）	突变：R118P	MG MAGNESIUM ION × 5	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；300 mM MgCl2, 15% PEG 400, and 100 mM Tris HCl	分辨率 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. 提交 2022-04-29	突变/修饰不同聚集状态不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：pentameric	链 C 1–251（251 aa）	突变：R118P	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；200 mM MgCl2, 30% PEG 400, 100 mM Tris HCl pH 8.0	分辨率 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. 提交 2022-05-06	突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	突变：R118P,L53G,Q54G,E55G	MG MAGNESIUM ION × 8	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；350 mM MgCl2, 30% PEG 400, and 100 mM Tris HCl	分辨率 3.15 Å R-free 0.264
8AAN The nucleoprotein complex of Rep protein with iteron containing dsDNA and DUE ssDNA. 提交 2022-07-01	聚集状态不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：tetrameric	链 A 1–251（251 aa）	未记录	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 2.19 Å R-free 0.233
8AC8 The nucleoprotein complex of Rep protein with DUE ssDNA 提交 2022-07-05	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：dimeric	链 C 1–251（251 aa）	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；291.15 K；PEG 8000, ethylene glycol, HEPES, halogens	分辨率 1.60 Å R-free 0.243
8AC8 The nucleoprotein complex of Rep protein with DUE ssDNA 提交 2022-07-05	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白–DNA 单体；蛋白 × 1 PDB 声明：dimeric	链 A 1–251（251 aa）	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；291.15 K；PEG 8000, ethylene glycol, HEPES, halogens	分辨率 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. 提交 2022-06-07	突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	突变：R118P	MG MAGNESIUM ION × 5 NT NETROPSIN × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；300 mM MgCl2, 25% PEG 400, and 100 mM Tris HCl	分辨率 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. 提交 2022-06-08	突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	突变：R118P	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；400 mM MgCl2, 24% PEG 400, and 80 mM Tris HCl	分辨率 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. 提交 2023-07-20	突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	突变：R118P	MG MAGNESIUM ION × 5	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；400 mM MgCl2, 25% PEG 400, and 100 mM Tris HCl	分辨率 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. 提交 2023-07-20	突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	突变：R118P	MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；350 mM MgCl2, 25% PEG 400, and 100 mM Tris HCl	分辨率 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. 提交 2023-07-20	突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	突变：R118P	MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；350 mM MgCl2, 30% PEG 400, and 100 mM Tris HCl	分辨率 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. 提交 2023-07-20	突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	突变：R118P	MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；350 mM MgCl2, 25% PEG 400, and 100 mM Tris HCl	分辨率 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. 提交 2023-07-20	突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	突变：R118P	MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；450 mM MgCl2, 25% PEG 400, and 100 mM Tris HCl	分辨率 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. 提交 2023-07-20	突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	突变：R118P	MG MAGNESIUM ION × 5	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；400 mM MgCl2, 30% PEG 400, and 100 mM Tris HCl	分辨率 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. 提交 2023-07-20	突变/修饰不同聚集状态不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	突变：R118P	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；350 mM MgCl2, 25% PEG 400, and 100 mM Tris HCl	分辨率 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. 提交 2023-07-20	聚集状态不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	未记录	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；350 mM MgCl2, 25% PEG 400, and 100 mM Tris HCl	分辨率 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. 提交 2023-07-20	突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	突变：R118P	MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；350 mM MgCl2, 30% PEG 400, and 100 mM Tris HCl	分辨率 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. 提交 2023-07-20	突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	突变：R118P	MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；350 mM MgCl2, 25% PEG 400, and 100 mM Tris HCl	分辨率 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. 提交 2023-07-20	突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	突变：R118P	MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；450 mM MgCl2, 25% PEG 400, and 100 mM Tris HCl	分辨率 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. 提交 2023-07-20	突变/修饰不同聚集状态不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	突变：R118P	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；400 mM MgCl2, 24% PEG 400, and 80 mM Tris HCl	分辨率 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. 提交 2023-07-20	突变/修饰不同聚集状态不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	突变：R118P	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；400 mM MgCl2, 30% PEG 400, and 100 mM Tris HCl	分辨率 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 提交 2025-02-13	聚集状态不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	未记录	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；500mM Lithium Sulfate, 20mM Magnesium Acetate, 50mM MES	分辨率 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 提交 2025-02-17	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	未记录	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；1M lithium sulfate, 30mM Magnesium acetate, 50mM MES	分辨率 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 提交 2025-10-30	突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	突变：L53G, Q54G, E55G	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；10 mM Magnesium acetate, 1300 mM Lithium sulfate, 50 mM MES pH 6.5	分辨率 3.05 Å R-free 0.309
9YZB Isoreticular co-crystal 1 with symmetrical expanded duplex (31mer) containing insert sequence ACGGTAATTA 提交 2025-10-30	聚集状态不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	未记录	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；10 mM Magnesium acetate, 1.6M Lithium sulfate, 50 mM MES pH 6.5	分辨率 4.13 Å R-free 0.253
9YZC Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence CGCGCGCGCG 提交 2025-10-30	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	未记录	MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；80 mM Magnesium acetate, 1.2 M Lithium sulfate, 50 mM MES pH 6.5	分辨率 3.16 Å R-free 0.299
9YZD Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence CTAATTAGGC 提交 2025-10-30	聚集状态不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	未记录	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；30 mM Magnesium acetate, 1.3 M Lithium sulfate, 50 mM MES pH 6.5	分辨率 3.09 Å R-free 0.265
9YZE Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence TGATGAGCAG 提交 2025-10-30	聚集状态不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	未记录	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；20 mM Magnesium acetate, 300 mM Lithium sulfate, 50 mM MES pH 6.5	分辨率 4.07 Å R-free 0.276
9YZF Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence AATTAGGCCG 提交 2025-10-30	聚集状态不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	未记录	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；50 mM Magnesium acetate, 1.1 M Lithium sulfate, 50 mM MES pH 6.5	分辨率 3.07 Å R-free 0.241
9YZG Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence ATGAGTCATA 提交 2025-10-30	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	未记录	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；20 mM Magnesium acetate, 1.4 M Lithium sulfate, 50 mM MES pH 6.5	分辨率 3.09 Å R-free 0.301
9YZI Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence CCCGGCCGGA 提交 2025-10-30	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	未记录	MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；50 mM Magnesium acetate, 1.6 M Lithium sulfate, 50 mM MES pH 6.5	分辨率 4.00 Å R-free 0.322
9YZJ Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence CGTAATTAGG 提交 2025-10-30	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	未记录	MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；30 mM Magnesium acetate, 1.7 M Lithium sulfate, 50 mM MES pH 6.5	分辨率 2.97 Å R-free 0.292
9YZK Isoreticular co-crystal 1 with symmetrical expanded duplex (42mer) containing insert sequence ACCCTTCTATGACCTACTCCA 提交 2025-10-30	聚集状态不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	未记录	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；298 K；60mM Magnesium acetate, 1.6M Lithium sulfate, 50mM MES pH 6.5	分辨率 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 提交 2025-10-30	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 异源复合物；蛋白 × 3 PDB 声明：pentameric	链 C 1–251（251 aa）	未记录	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 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 提交 2025-10-30	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 异源复合物；蛋白 × 3 PDB 声明：pentameric	链 C 1–251（251 aa）	未记录	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 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 提交 2025-10-30	实验环境不同结构质量不同	Assembly 1 蛋白–DNA 异源复合物；蛋白 × 3 PDB 声明：pentameric	链 C 1–251（251 aa）	未记录	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 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 提交 2025-10-30	实验环境不同结构质量不同	Assembly 1 蛋白–DNA 异源复合物；蛋白 × 3 PDB 声明：pentameric	链 C 1–251（251 aa）	未记录	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 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 提交 2025-10-30	聚集状态不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 异源复合物；蛋白 × 2 PDB 声明：tetrameric	链 C 1–251（251 aa）	未记录	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 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 提交 2025-10-30	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 信息不足异源复合物；蛋白 × 2 PDB 声明：tetrameric	链 C 1–251（251 aa）	未记录	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 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 提交 2025-10-30	实验环境不同结构质量不同	Assembly 1 蛋白–DNA 异源复合物；蛋白 × 3 PDB 声明：pentameric	链 C 1–251（251 aa）	未记录	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 3.39 Å R-free 0.298
9YZS Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence TAATTAGGCCG and loaded with Even-skipped homeodomain 提交 2025-10-30	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 异源复合物；蛋白 × 3 PDB 声明：pentameric	链 C 1–251（251 aa）	未记录	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 3.08 Å R-free 0.291
9YZU Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence ATGAGTCATA and loaded with mutated Bzip region of GCN4 transcription factor 提交 2025-10-30	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 异源复合物；蛋白 × 4 PDB 声明：hexameric	链 C 1–251（251 aa）	未记录	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 3.05 Å R-free 0.246
9Z08 Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing separate insert strand with sequence GACGGTAATT 提交 2025-10-31	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：pentameric	链 C 1–251（251 aa）	未记录	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 4.22 Å R-free 0.254
9Z1A Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence CCGCGCAGGC 提交 2025-11-03	聚集状态不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	未记录	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；80 mM Magnesium Acetate, 1.2 M Lithium Sulfate, 50 mM MES pH 6.5	分辨率 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 提交 2025-11-03	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	未记录	CA CALCIUM ION × 2 K POTASSIUM ION × 3 MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 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 提交 2025-11-03	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	未记录	K POTASSIUM ION × 3 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 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 提交 2025-11-03	聚集状态不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	未记录	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 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 提交 2025-11-08	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 异源复合物；蛋白 × 2 PDB 声明：tetrameric	链 C 1–251（251 aa）	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 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 提交 2025-11-10	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 异源复合物；蛋白 × 4 PDB 声明：hexameric	链 C 1–251（251 aa）	未记录	MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 3.63 Å R-free 0.285
9Z55 Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence CATGAGTCAT 提交 2025-11-11	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 C 1–251（251 aa）	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；40mM magnesium acetate, 1.8M lithium sulfate, 50mM MES pH 6.5	分辨率 3.94 Å R-free 0.316

共 57 个其他 PDB 条目、58 个 assembly。打开独立比较页并筛选聚集状态

查看构建体与数据证据

UniProt名称	REPE1_ECOLI
Isoform	—
PDB实体	3
链与序列区间	作者链 C； PDB构建体 13–263； UniProt 1–251

Homeotic protein antennapedia

Drosophila melanogaster

UniProt P02833

当前结构中的状态

Assembly	聚集状态	构建体	突变与修饰	配体、离子与共同组分	实验方法与环境	结构质量
1	蛋白–DNA 异源复合物蛋白 × 3 DNA 2 PDB 声明：pentameric（5）与全部聚合物数一致	链 D； UniProt 297–356 链 E； UniProt 297–356	未记录	DNA (31-MER) × 1 DNA (31-MER) × 1 Replication initiation protein × 1 （P03856） MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件：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.	分辨率 3.30 Å R-free 0.292

数据库中的同蛋白其他状态

其他 PDB	相对当前条目 9YZT	Assembly / 聚集状态	构建体	突变与修饰	配体、离子与非聚合物	实验方法与环境	结构质量
1HOM DETERMINATION OF THE THREE-DIMENSIONAL STRUCTURE OF THE ANTENNAPEDIA HOMEODOMAIN FROM DROSOPHILA IN SOLUTION BY 1H NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 提交 1991-10-08	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 297–363（67 aa）	未记录	未记录非水小分子	SOLUTION NMR mmCIF 未提供已读取条件	分辨率未提供
1KZ0 Solution structure of the third helix of Antennapedia homeodomain 提交 2002-02-06	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 50–65（16 aa）片段：C-terminal fragment of Antennapedia homeodomain	未记录	未记录非水小分子	SOLUTION NMR NMR测量条件 pH 3；300 K；压力 ambient NMR样品组成 1.5mM peptide; 90% TFEd2, 10% D2O \| 90% TFEd2, 10% D2O	分辨率未提供
1KZ5 Solution structure of the third helix of Antennapedia homeodomain derivatives (RQIKIWFRKWKK) 提交 2002-02-06	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 50–65（16 aa）	突变：DEL(Q57,N58,R60,M61)	未记录非水小分子	SOLUTION NMR NMR测量条件 pH 3；300 K；压力 ambient NMR样品组成 1.5mM peptide; 90% TFEd2, 10% D2O \| 90% TFEd2, 10% D2O	分辨率未提供
1OMQ Structure of penetratin in bicellar solution 提交 2003-02-26	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 339–354（16 aa）片段：C-terminal fragment	未记录	未记录非水小分子	SOLUTION NMR NMR测量条件 pH 5.5；310 K；离子强度（mmCIF原始值）50mM KCl；压力 1 NMR样品组成 3mM penetratin, 50 mM KCl; 15% w/v (DMPC+DMPG)/DHPC bicellar solution with q=0.5 and 5% D2O \| 15% w/v (DMPC+DMPG)/DHPC bicellar solution with q=0.5 and 5% D2O	分辨率未提供
1SAN THE DES(1-6)ANTENNAPEDIA HOMEODOMAIN: COMPARISON OF THE NMR SOLUTION STRUCTURE AND THE DNA BINDING AFFINITY WITH THE INTACT ANTENNAPEDIA HOMEODOMAIN 提交 1994-01-07	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 303–363（61 aa）	未记录	未记录非水小分子	SOLUTION NMR mmCIF 未提供已读取条件	分辨率未提供
2HOA STRUCTURE DETERMINATION OF THE ANTP(C39->S) HOMEODOMAIN FROM NUCLEAR MAGNETIC RESONANCE DATA IN SOLUTION USING A NOVEL STRATEGY FOR THE STRUCTURE CALCULATION WITH THE PROGRAMS DIANA, CALIBA, HABAS AND GLOMSA 提交 1992-04-04	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 297–363（67 aa）	未记录	未记录非水小分子	SOLUTION NMR mmCIF 未提供已读取条件	分辨率未提供
4XIC ANTPHD WITH 15BP di-thioate modified DNA DUPLEX 提交 2015-01-06	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 297–356（60 aa）片段：UNP residues 297-356	未记录	NI NICKEL (II) ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；300 K；20 mM BTP, 10 mM NiCl, 5% MPD	分辨率 2.69 Å R-free 0.272
4XIC ANTPHD WITH 15BP di-thioate modified DNA DUPLEX 提交 2015-01-06	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 D 297–356（60 aa）片段：UNP residues 297-356	未记录	NI NICKEL (II) ION × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；300 K；20 mM BTP, 10 mM NiCl, 5% MPD	分辨率 2.69 Å R-free 0.272
4XID AntpHD with 15bp DNA duplex 提交 2015-01-06	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 297–356（60 aa）片段：UNP residues 297-356	未记录	NI NICKEL (II) ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；300 K；20 mM BTP, 10 mM NiCl, 5% MPD	分辨率 2.70 Å R-free 0.274
4XID AntpHD with 15bp DNA duplex 提交 2015-01-06	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 D 297–356（60 aa）片段：UNP residues 297-356	未记录	NI NICKEL (II) ION × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；300 K；20 mM BTP, 10 mM NiCl, 5% MPD	分辨率 2.70 Å R-free 0.274
5JLW AntpHD with 15bp DNA duplex R-monothioated at Cytidine-8 提交 2016-04-27	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 297–356（60 aa）	突变：C335S	NI NICKEL (II) ION × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；20mM bis-Tris propane, 10mM NiCl2, 4-6% 2-methyl-2,4-pentanediol	分辨率 2.09 Å R-free 0.242
5JLW AntpHD with 15bp DNA duplex R-monothioated at Cytidine-8 提交 2016-04-27	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 D 297–356（60 aa）	突变：C335S	NI NICKEL (II) ION × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；20mM bis-Tris propane, 10mM NiCl2, 4-6% 2-methyl-2,4-pentanediol	分辨率 2.09 Å R-free 0.242
5JLX AntpHD with 15bp DNA duplex S-monothioated at Cytidine-8 提交 2016-04-27	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 297–356（60 aa）	突变：C335S	NI NICKEL (II) ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；20mM bis-Tris propane, 10mM NiCl2, 4-6% 2-methyl-2,4-pentanediol	分辨率 2.75 Å R-free 0.246
5JLX AntpHD with 15bp DNA duplex S-monothioated at Cytidine-8 提交 2016-04-27	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 D 297–356（60 aa）	突变：C335S	NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；20mM bis-Tris propane, 10mM NiCl2, 4-6% 2-methyl-2,4-pentanediol	分辨率 2.75 Å R-free 0.246
9ANT ANTENNAPEDIA HOMEODOMAIN-DNA COMPLEX 提交 1998-07-02	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 A 1–60（60 aa）片段：HOMEODOMAIN	突变：C39S	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 pH 7；1-5% MPD 20 MM BIS-TRIS-PROPANE, PH 7.0 10 MM NICL2	分辨率 2.40 Å R-free 0.239
9ANT ANTENNAPEDIA HOMEODOMAIN-DNA COMPLEX 提交 1998-07-02	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白–DNA 单体；蛋白 × 1 PDB 声明：trimeric	链 B 1–60（60 aa）片段：HOMEODOMAIN	突变：C39S	NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray结晶条件 pH 7；1-5% MPD 20 MM BIS-TRIS-PROPANE, PH 7.0 10 MM NICL2	分辨率 2.40 Å R-free 0.239

共 11 个其他 PDB 条目、16 个 assembly。打开独立比较页并筛选聚集状态

查看构建体与数据证据

UniProt名称	ANTP_DROME
Isoform	—
PDB实体	4
链与序列区间	作者链 D； PDB构建体 3–62； UniProt 297–356 作者链 E； PDB构建体 3–62； UniProt 297–356

页面优先展示蛋白身份、当前 assembly、共同组分、聚集状态和跨 PDB 结构链接。链映射与序列区间收在“数据证据”中；数据库内部编号、导入时间和 assembly 操作表达式仅用于维护，因此不在读者页面展示。

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

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

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	9yzt
沉积日期 deposition_date	2025-10-30
最后修订 last_revision	2026-02-18
结构标题 title	Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence TAATTAGGCCG and loaded with Antennapedia homeodomain
关键词 keywords	Protein-DNA complex, DNA Binding protein, Transcription factor; DNA BINDING PROTEIN
实验方法 method	X-RAY DIFFRACTION

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3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	27.93 Å
回转半径 Rg (电子) rg_electron	26.80 Å
零角强度 I(0) i0	69252000.00
分子量 molecular_weight	52175.0 kDa
排除体积 excluded_volume	59505 Å³
包络体积 envelope_volume	82418 Å³
水化壳体积 shell_volume	27260 Å³
包络直径 envelope_diameter	102.3 Å
壳层 Rg shell_rg	31.74 Å
包络 Rg envelope_rg	27.22 Å
形状 Rg shape_rg	26.69 Å
总 Rg total_rg	27.47 Å
总原子数 total_atoms	3606
残基数 n_residues	377
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	99.8 Å
Rg (实空间) rg_real	28.24 Å
Rg 误差 (实空间) rg_real_error	0.99 Å
I(0) (实空间) i0_real	6.9250e+07
I(0) 误差 (实空间) i0_real_error	1.1380e+06
Rg (倒空间) rg_reciprocal	28.14 Å
I(0) (倒空间) i0_reciprocal	69250000.0000
解质量估计 total_estimate	0.8363
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	29.8 Å
偏度 Skewness skewness	0.643
峰度 Kurtosis kurtosis	0.175
角度范围 angular_range	— – 0.2850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	6337000.0000
实空间数据点数 n_real_points	58
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.714; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.803; Smooth: 0.923

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5. 晶体学与实验 5. Crystallography & Experiment

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6. 实体与聚合物信息 Entities & Polymers (5)

实体 1 Entity 1 polymer

描述 description	DNA (31-MER)
分子量 formula_weight	9472.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合物 Polymer

聚合物类型 type	polydeoxyribonucleotide
链编号 strand_id	A
原子数 atom_count	3624

CCTGTGACAAATTGCCCTCATAATTAGGCCG

实体 2 Entity 2 polymer

描述 description	DNA (31-MER)
分子量 formula_weight	9592.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合物 Polymer

聚合物类型 type	polydeoxyribonucleotide
链编号 strand_id	B

GCGGCCTAATTATGAGGGCAATTTGTCACAG

实体 3 Entity 3 polymer

描述 description	Replication initiation protein
分子量 formula_weight	30749.1 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	C

MRGSHHHHHHGSMAETAVINHKKRKNSPRIVQSNDLTEAAYSLSRDQKRMLYLFVDQIRKSDGTLQEHDGICEIHVAKYAEIFGLTSAEASKDIRQALKSFAGKEVVFYRPEEDAGDEKGYESFPWFIKPAHSPSRGLYSVHINPYLIPFFIGLQNRFTQFRLSETKEITNPYAMRLYESLCQYRKPDGSGIVSLKIDWIIERYQLPQSYQRMPDFRRRFLQVCVNEINSRTPMRLSYIEKKKGRQTTHIVFSFRDITSMTTG

来源 Source

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

实体 4 Entity 4 polymer

描述 description	Homeotic protein antennapedia
分子量 formula_weight	8004.3 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	D,E

GTRKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN

来源 Source

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

实体 5 Entity 5 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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8. 引用文献 (2)

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晶胞边长 a length_a	72.747 Å
晶胞边长 b length_b	126.040 Å
晶胞边长 c length_c	134.954 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.24 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	I 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	monoclinic

分辨率 resolution	3.300 Å
最低分辨率 resolution_low	46.130 Å
R 因子 r_factor	0.2837
R_work r_work	0.2827
R_free r_free	0.2921

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

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

1. 蛋白身份与相关结构 Protein Identity & Related Structures

Replication initiation protein

当前结构中的状态

数据库中的同蛋白其他状态

Homeotic protein antennapedia

当前结构中的状态

数据库中的同蛋白其他状态

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

2. 结构基本信息 2. Structure Basics

3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

5. 晶体学与实验 5. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

6. 实体与聚合物信息 Entities & Polymers (5)

实体 1 Entity 1 polymer

聚合物 Polymer

实体 2 Entity 2 polymer

聚合物 Polymer

实体 3 Entity 3 polymer

聚合物 Polymer

来源 Source

实体 4 Entity 4 polymer

聚合物 Polymer

来源 Source

实体 5 Entity 5 non-polymer

8. 引用文献 (2)

9. 文件与曲线 (10)

Files (7)

Curves (3)