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1bbx

NON-SPECIFIC PROTEIN-DNA INTERACTIONS IN THE SSO7D-DNA COMPLEX, NMR, 1 STRUCTURE

Method: SOLUTION NMR Dmax: 60.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-BINDING PROTEIN 7D

Sulfolobus solfataricus

UniProt P39476

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 Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain C； UniProt 1–63 Chain D； UniProt 1–63 Not recorded ;DNA (5'-D(*CP*TP*AP*GP*CP*GP*CP*GP*CP*TP*AP*G)-3') ; × 2 SOLUTION NMR NMR measurement conditions：pH 5；323 K；Ionic strength (raw mmCIF value) 60 mM；Pressure 1 NMR sample composition：H2O:D2O 9:1 Resolution not provided

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 1BBX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1C8C CRYSTAL STRUCTURES OF THE CHROMOSOMAL PROTEINS SSO7D/SAC7D BOUND TO DNA CONTAINING T-G MISMATCHED BASE PAIRS Deposited 2000-05-04 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–64（64 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；PROTEIN WAS CRYSTALLIZED FROM 1.3MM SSO7D, 1.3MM DUPLEX DNA, 2.5 MM TRIS (PH 6.5), 2.5% PEG 400, EQUILIBRATED AGAINST 15% PEG 400 at pH 6.5, VAPOR DIFFUSION, HANGING DROP
Resolution 1.45 Å R-free 0.287
1JIC SOLUTION NMR STRUCTURE OF RECOMBINANT SSO7D WITH RNASE ACTIVITY, MINIMIZED AVERAGE STRUCTURE Deposited 1998-07-20 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–62（62 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.5；300 K
NMR sample composition H2O
Resolution not provided
5B02 Structure of the prenyltransferase MoeN5 with a fusion protein tag of Sso7d Deposited 2015-10-27 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–64（64 aa）
Chain B 1–64（64 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350
Resolution 2.21 Å R-free 0.218
5B02 Structure of the prenyltransferase MoeN5 with a fusion protein tag of Sso7d Deposited 2015-10-27 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–64（64 aa）
Chain D 1–64（64 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350
Resolution 2.21 Å R-free 0.218
5B03 Structure of MoeN5-Sso7d fusion protein in complex with geranyl pyrophosphate Deposited 2015-10-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–64（64 aa）
Chain B 1–64（64 aa）
Not recorded GPP GERANYL DIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 5mM GPP, 0.3M Li3-citrate, 0.4M NaCl, 27% PEG 3350, 5% glycerol
Resolution 2.60 Å R-free 0.239
5B03 Structure of MoeN5-Sso7d fusion protein in complex with geranyl pyrophosphate Deposited 2015-10-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–64（64 aa）
Chain D 1–64（64 aa）
Not recorded GPP GERANYL DIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 5mM GPP, 0.3M Li3-citrate, 0.4M NaCl, 27% PEG 3350, 5% glycerol
Resolution 2.60 Å R-free 0.239
5B0I Structure of MoeN5-Sso7d fusion protein in complex with beta-octyl glucoside Deposited 2015-10-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–64（64 aa）
Chain B 1–64（64 aa）
Not recorded BOG octyl beta-D-glucopyranoside × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 5% Glycerol, 1% beta-octyl glucoside
Resolution 2.26 Å R-free 0.229
5B0I Structure of MoeN5-Sso7d fusion protein in complex with beta-octyl glucoside Deposited 2015-10-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–64（64 aa）
Chain D 1–64（64 aa）
Not recorded BOG octyl beta-D-glucopyranoside × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 5% Glycerol, 1% beta-octyl glucoside
Resolution 2.26 Å R-free 0.229
5B0J Structure of MoeN5-Sso7d fusion protein in complex with beta-undecyl maltoside Deposited 2015-10-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–64（64 aa）
Chain B 1–64（64 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 1% undecylmaltoside
Resolution 2.50 Å R-free 0.238
5B0J Structure of MoeN5-Sso7d fusion protein in complex with beta-undecyl maltoside Deposited 2015-10-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–64（64 aa）
Chain D 1–64（64 aa）
Not recorded UMQ UNDECYL-MALTOSIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 1% undecylmaltoside
Resolution 2.50 Å R-free 0.238
5B0K Structure of MoeN5-Sso7d fusion protein in complex with beta-decyl maltoside Deposited 2015-10-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–64（64 aa）
Chain B 1–64（64 aa）
Not recorded DMU DECYL-BETA-D-MALTOPYRANOSIDE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 5% glycerol, 1% beta-decyl-D-maltoside
Resolution 2.75 Å R-free 0.248
5B0K Structure of MoeN5-Sso7d fusion protein in complex with beta-decyl maltoside Deposited 2015-10-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–64（64 aa）
Chain D 1–64（64 aa）
Not recorded DMU DECYL-BETA-D-MALTOPYRANOSIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 5% glycerol, 1% beta-decyl-D-maltoside
Resolution 2.75 Å R-free 0.248
5B0L Structure of MoeN5-Sso7d fusion protein in complex with beta-nonyl glucoside Deposited 2015-11-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–64（64 aa）
Chain B 1–64（64 aa）
Not recorded BNG nonyl beta-D-glucopyranoside × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 1% beta-nonyl-D-glucoside
Resolution 2.80 Å R-free 0.232
5B0L Structure of MoeN5-Sso7d fusion protein in complex with beta-nonyl glucoside Deposited 2015-11-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–64（64 aa）
Chain D 1–64（64 aa）
Not recorded BNG nonyl beta-D-glucopyranoside × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 1% beta-nonyl-D-glucoside
Resolution 2.80 Å R-free 0.232
5B0L Structure of MoeN5-Sso7d fusion protein in complex with beta-nonyl glucoside Deposited 2015-11-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 1–64（64 aa）
Chain F 1–64（64 aa）
Not recorded BNG nonyl beta-D-glucopyranoside × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 1% beta-nonyl-D-glucoside
Resolution 2.80 Å R-free 0.232
5B0L Structure of MoeN5-Sso7d fusion protein in complex with beta-nonyl glucoside Deposited 2015-11-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain G 1–64（64 aa）
Chain H 1–64（64 aa）
Not recorded BNG nonyl beta-D-glucopyranoside × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 1% beta-nonyl-D-glucoside
Resolution 2.80 Å R-free 0.232
5B0M Structure of MoeN5-Sso7d fusion protein in complex with beta-dodecyl maltoside Deposited 2015-11-02 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–64（64 aa）
Chain B 1–64（64 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 1% beta-dodecyl-D-maltoside
Resolution 3.05 Å R-free 0.249
5B0M Structure of MoeN5-Sso7d fusion protein in complex with beta-dodecyl maltoside Deposited 2015-11-02 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–64（64 aa）
Chain D 1–64（64 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 1% beta-dodecyl-D-maltoside
Resolution 3.05 Å R-free 0.249
5B0M Structure of MoeN5-Sso7d fusion protein in complex with beta-dodecyl maltoside Deposited 2015-11-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 1–64（64 aa）
Chain F 1–64（64 aa）
Not recorded LMT DODECYL-BETA-D-MALTOSIDE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 1% beta-dodecyl-D-maltoside
Resolution 3.05 Å R-free 0.249
5B0M Structure of MoeN5-Sso7d fusion protein in complex with beta-dodecyl maltoside Deposited 2015-11-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain G 1–64（64 aa）
Chain H 1–64（64 aa）
Not recorded LMT DODECYL-BETA-D-MALTOSIDE × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 1% beta-dodecyl-D-maltoside
Resolution 3.05 Å R-free 0.249
5GWV Structure of MoeN5-Sso7d fusion protein in complex with a substrate analogue Deposited 2016-09-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–64（64 aa）
Chain B 1–64（64 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；Protein: 10mg/mL in 10mM DTT, 1mM MgCl2 Reservoir: 0.2M Li3-citrate, 0.3M NaCl, 25% w/v PEG 3350 Cryoprotectant: 5mM substrate analogue in 0.3M Li3-citrate, 0.4M NaCl, 27% w/v PEG 3350, 5% glycerol
Resolution 2.40 Å R-free 0.216
5GWV Structure of MoeN5-Sso7d fusion protein in complex with a substrate analogue Deposited 2016-09-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–64（64 aa）
Chain D 1–64（64 aa）
Not recorded 78S (2R)-3-dimethoxyphosphoryloxy-2-[(2Z,6E)-3,7,11-trimethyldodeca-2,6,10-trienoxy]propanoic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；Protein: 10mg/mL in 10mM DTT, 1mM MgCl2 Reservoir: 0.2M Li3-citrate, 0.3M NaCl, 25% w/v PEG 3350 Cryoprotectant: 5mM substrate analogue in 0.3M Li3-citrate, 0.4M NaCl, 27% w/v PEG 3350, 5% glycerol
Resolution 2.40 Å R-free 0.216
5GWW Structure of MoeN5-Sso7d fusion protein in complex with a permethylated substrate analogue Deposited 2016-09-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–64（64 aa）
Chain B 1–64（64 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；protein: 10 mg/mL in 10 mM DTT, 1 mM MgCl2 reservoir: 0.2 M Li3 citrate, 0.3 M NaCl, 25% w/v PEG 3350 cryoprotectant: 5 mM permethylated analogue, 0.3 M Li3 citrate, 0.4 M NaCl, 27% w/v PEG 3350, 5% glycerol
Resolution 2.30 Å R-free 0.221
5GWW Structure of MoeN5-Sso7d fusion protein in complex with a permethylated substrate analogue Deposited 2016-09-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–64（64 aa）
Chain D 1–64（64 aa）
Not recorded 7B5 methyl (2R)-3-dimethoxyphosphoryloxy-2-[(2Z,6E)-3,7,11-trimethyldodeca-2,6,10-trienoxy]propanoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；protein: 10 mg/mL in 10 mM DTT, 1 mM MgCl2 reservoir: 0.2 M Li3 citrate, 0.3 M NaCl, 25% w/v PEG 3350 cryoprotectant: 5 mM permethylated analogue, 0.3 M Li3 citrate, 0.4 M NaCl, 27% w/v PEG 3350, 5% glycerol
Resolution 2.30 Å R-free 0.221
6J8V Structure of MOEN5-SSO7D fusion protein in complex with ligand 2 Deposited 2019-01-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–64（64 aa）
Chain B 1–64（64 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M LI3-CITRATE, 0.3M NACL, 25% W/V PEG 3350
Resolution 2.23 Å R-free 0.225
6J8V Structure of MOEN5-SSO7D fusion protein in complex with ligand 2 Deposited 2019-01-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–64（64 aa）
Chain D 1–64（64 aa）
Not recorded FAR FARNESYL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M LI3-CITRATE, 0.3M NACL, 25% W/V PEG 3350
Resolution 2.23 Å R-free 0.225
6J8W Structure of MOEN5-SSO7D fusion protein in complex with lig 1 Deposited 2019-01-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–64（64 aa）
Chain B 1–64（64 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M LI3-CITRATE, 0.3M NACL, 25% W/V PEG 3350
Resolution 2.35 Å R-free 0.225
6J8W Structure of MOEN5-SSO7D fusion protein in complex with lig 1 Deposited 2019-01-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–64（64 aa）
Chain D 1–64（64 aa）
Not recorded C0X (2S)-3-dimethoxyphosphoryloxy-2-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienoxy]propanoic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M LI3-CITRATE, 0.3M NACL, 25% W/V PEG 3350
Resolution 2.35 Å R-free 0.225
6PUT Structure of HIV cleaved synaptic complex (CSC) intasome bound with calcium Deposited 2019-07-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 8 PDB declaration: dodecameric
Chain A 1–64（64 aa）
Chain B 1–64（64 aa）
Chain C 1–64（64 aa）
Chain D 1–64（64 aa）
Not recorded CA CALCIUM ION × 4 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å R-free 0.536
6PUT Structure of HIV cleaved synaptic complex (CSC) intasome bound with calcium Deposited 2019-07-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric
Chain A 1–64（64 aa）
Chain B 1–64（64 aa）
Chain C 1–64（64 aa）
Chain D 1–64（64 aa）
Not recorded CA CALCIUM ION × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å R-free 0.536
6PUT Structure of HIV cleaved synaptic complex (CSC) intasome bound with calcium Deposited 2019-07-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric
Chain A 1–64（64 aa）
Chain B 1–64（64 aa）
Chain C 1–64（64 aa）
Chain D 1–64（64 aa）
Not recorded CA CALCIUM ION × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å R-free 0.536
6PUW Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and Bictegravir (BIC) Deposited 2019-07-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 8 PDB declaration: dodecameric
Chain A 1–64（64 aa）
Chain B 1–64（64 aa）
Chain C 1–64（64 aa）
Chain D 1–64（64 aa）
Not recorded MG MAGNESIUM ION × 4 ZN ZINC ION × 4 KLQ Bictegravir × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å R-free 0.534
6PUW Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and Bictegravir (BIC) Deposited 2019-07-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric
Chain A 1–64（64 aa）
Chain B 1–64（64 aa）
Chain C 1–64（64 aa）
Chain D 1–64（64 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 2 KLQ Bictegravir × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å R-free 0.534
6PUW Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and Bictegravir (BIC) Deposited 2019-07-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric
Chain A 1–64（64 aa）
Chain B 1–64（64 aa）
Chain C 1–64（64 aa）
Chain D 1–64（64 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 2 KLQ Bictegravir × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å R-free 0.534
6PUY Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ426 (compound 4d) Deposited 2019-07-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 8 PDB declaration: dodecameric
Chain A 1–64（64 aa）
Chain B 1–64（64 aa）
Chain C 1–64（64 aa）
Chain D 1–64（64 aa）
Not recorded MG MAGNESIUM ION × 4 ZN ZINC ION × 4 OZ1 4-amino-N-[(2,4-difluorophenyl)methyl]-1-hydroxy-6-(6-hydroxyhexyl)-2-oxo-1,2-dihydro-1,8-naphthyridine-3-carboxamide × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å R-free 0.516
6PUY Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ426 (compound 4d) Deposited 2019-07-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric
Chain A 1–64（64 aa）
Chain B 1–64（64 aa）
Chain C 1–64（64 aa）
Chain D 1–64（64 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 2 OZ1 4-amino-N-[(2,4-difluorophenyl)methyl]-1-hydroxy-6-(6-hydroxyhexyl)-2-oxo-1,2-dihydro-1,8-naphthyridine-3-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å R-free 0.516
6PUY Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ426 (compound 4d) Deposited 2019-07-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric
Chain A 1–64（64 aa）
Chain B 1–64（64 aa）
Chain C 1–64（64 aa）
Chain D 1–64（64 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 2 OZ1 4-amino-N-[(2,4-difluorophenyl)methyl]-1-hydroxy-6-(6-hydroxyhexyl)-2-oxo-1,2-dihydro-1,8-naphthyridine-3-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å R-free 0.516
6PUZ Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ446 (compound 4f) Deposited 2019-07-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 8 PDB declaration: dodecameric
Chain A 1–64（64 aa）
Chain B 1–64（64 aa）
Chain C 1–64（64 aa）
Chain D 1–64（64 aa）
Not recorded MG MAGNESIUM ION × 4 ZN ZINC ION × 4 XXJ 4-azanyl-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-6-[2-(phenylsulfonyl)ethyl]-1,8-naphthyridine-3-carboxamide × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å R-free 0.535
6PUZ Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ446 (compound 4f) Deposited 2019-07-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric
Chain A 1–64（64 aa）
Chain B 1–64（64 aa）
Chain C 1–64（64 aa）
Chain D 1–64（64 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 2 XXJ 4-azanyl-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-6-[2-(phenylsulfonyl)ethyl]-1,8-naphthyridine-3-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å R-free 0.535
6PUZ Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ446 (compound 4f) Deposited 2019-07-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric
Chain A 1–64（64 aa）
Chain B 1–64（64 aa）
Chain C 1–64（64 aa）
Chain D 1–64（64 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 2 XXJ 4-azanyl-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-6-[2-(phenylsulfonyl)ethyl]-1,8-naphthyridine-3-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å R-free 0.535
6V3K Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ419 (compound 4c) Deposited 2019-11-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 8 PDB declaration: dodecameric
Chain A 1–64（64 aa）
Chain B 1–64（64 aa）
Chain C 1–64（64 aa）
Chain D 1–64（64 aa）
Not recorded MG MAGNESIUM ION × 4 ZN ZINC ION × 4 QUW 4-azanyl-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-6-(5-oxidanylpentyl)-1,8-naphthyridine-3-carboxamide × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å R-free 0.555
6V3K Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ419 (compound 4c) Deposited 2019-11-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric
Chain A 1–64（64 aa）
Chain B 1–64（64 aa）
Chain C 1–64（64 aa）
Chain D 1–64（64 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 2 QUW 4-azanyl-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-6-(5-oxidanylpentyl)-1,8-naphthyridine-3-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å R-free 0.555
6V3K Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ419 (compound 4c) Deposited 2019-11-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric
Chain A 1–64（64 aa）
Chain B 1–64（64 aa）
Chain C 1–64（64 aa）
Chain D 1–64（64 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 2 QUW 4-azanyl-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-6-(5-oxidanylpentyl)-1,8-naphthyridine-3-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å R-free 0.555
6VOY Cryo-EM structure of HTLV-1 instasome Deposited 2020-02-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: dodecameric
Chain A 1–64（64 aa）
Chain B 1–64（64 aa）
Chain C 1–64（64 aa）
Chain D 1–64（64 aa）
Mutation：W24A Mutation：W24A Mutation：W24A Mutation：W24A ZN ZINC ION × 4 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.70 Å

19 other PDB entries and 44 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DN72_SULSO
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–63； UniProt 1–63 Author chain D； PDBConstruct 1–63； UniProt 1–63

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

SAXS profile for 1bbx

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1bbx
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1bbx
Deposition date deposition_date1998-04-24
Structure title titleNON-SPECIFIC PROTEIN-DNA INTERACTIONS IN THE SSO7D-DNA COMPLEX, NMR, 1 STRUCTURE
Keywords keywordsPROTEIN-DNA INTERACTION, NONSPECIFIC PROTEIN-DNA INTERACTION, COMPLEX (DNA-BINDING PROTEIN-DNA), DNA BINDING PROTEIN-DNA COMPLEX; DNA BINDING PROTEIN/DNA
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier18.19 Å
Radius of gyration Rg (electron density) rg_electron17.99 Å
Forward intensity I(0) i011801300.00
Molecular weight molecular_weight21622.0 kDa
Excluded volume excluded_volume25317 ų
Envelope volume envelope_volume31541 ų
Hydration-shell volume shell_volume15075 ų
Envelope diameter envelope_diameter60.1 Å
Shell Rg shell_rg23.44 Å
Envelope Rg envelope_rg18.25 Å
Shape Rg shape_rg17.98 Å
Total Rg total_rg18.76 Å
Total atoms total_atoms2834
Residues n_residues150
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax60.1 Å
Rg (real space) rg_real18.17 Å
Rg uncertainty (real space) rg_real_error0.35 Å
I(0) (real space) i0_real1.1800e+07
I(0) uncertainty (real space) i0_real_error1.4350e+05
Rg (reciprocal space) rg_reciprocal18.17 Å
I(0) (reciprocal space) i0_reciprocal11800000.0000
Solution quality estimate total_estimate0.8927
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.3 Å
Skewness Skewness skewness0.310
Kurtosis Kurtosis kurtosis-0.367
Angular range angular_range— – 0.4350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1461000.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.875; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.985
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1bbxc_
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.13 — Chromo domain-like
Family Family familyb.34.13.1 — Histone-like proteins from archaea
Domain ID domain_idd1bbxd_
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.13 — Chromo domain-like
Family Family familyb.34.13.1 — Histone-like proteins from archaea

CATH v4.4 (2 domains)

Domain ID domain_id1bbxC00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily40 —
Domain ID domain_id1bbxD00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily40 —
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8. Citations (3)

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9. Files and Curves (10)