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1dbq

DNA-BINDING REGULATORY PROTEIN

Method: X-RAY DIFFRACTION Dmax: 82.6 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PURINE REPRESSOR

OrganismNot specified

UniProt P0ACP7

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 52–340 Chain B； UniProt 52–340 Fragment：COREPRESSOR-FREE COREPRESSOR-BINDING DOMAIN MG MAGNESIUM ION × 3 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.20 Å

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 1DBQ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BDH PURINE REPRESSOR MUTANT-HYPOXANTHINE-PALINDROMIC OPERATOR COMPLEX Deposited 1996-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 1–340（340 aa）
Mutation：K55A HPA HYPOXANTHINE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å
1BDI PURINE REPRESSOR MUTANT-HYPOXANTHINE-PALINDROMIC OPERATOR COMPLEX Deposited 1996-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 1–340（340 aa）
Not recorded HPA HYPOXANTHINE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
1JFS PURINE REPRESSOR MUTANT-HYPOXANTHINE-PURF OPERATOR COMPLEX Deposited 2001-06-21 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 1–340（340 aa）
Mutation：W147F HPA HYPOXANTHINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；PEG 4000, ammonium phosphate, ammonium sulfate, cobalt hexammine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.90 Å
1JFT PURINE REPRESSOR MUTANT-HYPOXANTHINE-PURF OPERATOR COMPLEX Deposited 2001-06-21 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 1–340（340 aa）
Mutation：W147A PO4 PHOSPHATE ION × 2 HPA HYPOXANTHINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG 4000, ammonuim sulfate, ammonium phosphate, cobalt hexammine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å
1JH9 PURINE REPRESSOR MUTANT-HYPOXANTHINE-PURF OPERATOR COMPLEX Deposited 2001-06-27 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 1–340（340 aa）
Mutation：W147R PO4 PHOSPHATE ION × 4 HPA HYPOXANTHINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG 4000, ammonium sulfate, ammonium phosphate, cobalt hexammine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.55 Å
1JHZ Purine Repressor Mutant Corepressor Binding Domain Structure Deposited 2001-06-28 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 52–340（289 aa） Fragment：COREPRESSOR-FREE COREPRESSOR BINDING DOMAIN (Residues 53-341)
Chain B 52–340（289 aa） Fragment：COREPRESSOR-FREE COREPRESSOR BINDING DOMAIN (Residues 53-341)
Mutation：W147F Mutation：W147F MG MAGNESIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；298 K；PEG 600, magnesium chloride, Tris HCl, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å
1PNR PURINE REPRESSOR-HYPOXANTHINE-PURF-OPERATOR COMPLEX Deposited 1995-03-29 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 1–340（340 aa）
Not recorded HPA HYPOXANTHINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；VAPOR DIFFUSION, HANGING DROP, temperature 293.00K
Resolution 2.70 Å
1PRU PURINE REPRESSOR DNA-BINDING DOMAIN DNA BINDING Deposited 1995-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–55（55 aa） Fragment：DNA-BINDING
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1PRV PURINE REPRESSOR DNA-BINDING DOMAIN DNA BINDING Deposited 1995-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–55（55 aa） Fragment：DNA-BINDING
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1QP0 PURINE REPRESSOR-HYPOXANTHINE-PALINDROMIC OPERATOR COMPLEX Deposited 1999-06-01 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 1–340（340 aa）
Not recorded HPA HYPOXANTHINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG 4000, (NH4)2SO4, [Co(NH3)6]Cl3, Na2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.90 Å
1QP4 PURINE REPRESSOR-HYPOXANTHINE-PALINDROMIC OPERATOR COMPLEX Deposited 1999-06-01 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 1–340（340 aa）
Not recorded HPA HYPOXANTHINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG 4000, (NH4)2SO4, [CO(NH3)6]CL3, NA2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.00 Å
1QP7 PURINE REPRESSOR MUTANT-HYPOXANTHINE-PALINDROMIC OPERATOR COMPLEX Deposited 1999-06-01 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 1–340（340 aa）
Mutation：K55A HPA HYPOXANTHINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG 4000, (NH4)3PO4, [CO(NH3)6]CL3, NA2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.90 Å
1QPZ PURINE REPRESSOR-HYPOXANTHINE-PALINDROMIC OPERATOR COMPLEX Deposited 1999-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 1–340（340 aa）
Not recorded HPA HYPOXANTHINE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
1QQA PURINE REPRESSOR MUTANT-HYPOXANTHINE-PALINDROMIC OPERATOR COMPLEX Deposited 1999-06-01 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 1–340（340 aa）
Mutation：K55A HPA HYPOXANTHINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG 4000, (NH4)3PO4, (NH4)2SO4, [CO(NH3)6]CL3, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.00 Å
1QQB PURINE REPRESSOR MUTANT-HYPOXANTHINE-PALINDROMIC OPERATOR COMPLEX Deposited 1999-06-01 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 1–340（340 aa）
Not recorded HPA HYPOXANTHINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG 4000, (NH4)3PO4, (NH4)2SO4, [CO(NH3)6]CL3, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.70 Å
1VPW STRUCTURE OF THE PURR MUTANT, L54M, BOUND TO HYPOXANTHINE AND PURF OPERATOR DNA Deposited 1998-02-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 1–340（340 aa）
Mutation：L54M HPA HYPOXANTHINE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å
1WET STRUCTURE OF THE PURR-GUANINE-PURF OPERATOR COMPLEX Deposited 1997-04-27 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 1–340（340 aa）
Not recorded GUN GUANINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；pH 7.50, VAPOR DIFFUSION, HANGING DROP
Resolution 2.60 Å
1ZAY PURINE REPRESSOR-HYPOXANTHINE-MODIFIED-PURF-OPERATOR COMPLEX Deposited 1998-12-16 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 1–340（340 aa）
Not recorded HPA HYPOXANTHINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；pH 7.5, VAPOR DIFFUSION, HANGING DROP
Resolution 2.70 Å
2PUA CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: MINOR GROOVE BINDING BY ALPHA HELICES Deposited 1997-10-04 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 1–340（340 aa）
Mutation：R190A 6MP 6-METHYLPURINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；pH 7.40, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K
Resolution 2.90 Å
2PUB CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: MINOR GROOVE BINDING BY ALPHA HELICES Deposited 1997-10-04 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 1–340（340 aa）
Mutation：R190A ADE ADENINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；pH 7.40, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K
Resolution 2.70 Å
2PUC CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: MINOR GROOVE BINDING BY ALPHA HELICES Deposited 1997-10-04 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 1–340（340 aa）
Mutation：R190A GUN GUANINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；pH 7.40, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K
Resolution 2.60 Å
2PUD CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: MINOR GROOVE BINDING BY ALPHA HELICES Deposited 1997-10-04 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 1–340（340 aa）
Mutation：R190Q HPA HYPOXANTHINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K
Resolution 2.60 Å
2PUE CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: MINOR GROOVE BINDING BY ALPHA HELICES Deposited 1997-10-04 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 1–340（340 aa）
Mutation：R190Q ADE ADENINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；pH 7.40, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K
Resolution 2.70 Å
2PUF CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: MINOR GROOVE BINDING BY ALPHA HELICES Deposited 1997-10-04 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 1–340（340 aa）
Mutation：R190Q GUN GUANINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；pH 7.40, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K
Resolution 3.00 Å
2PUG CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: MINOR GROOVE BINDING BY ALPHA HELICES Deposited 1997-10-04 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 1–340（340 aa）
Mutation：R190Q HPA HYPOXANTHINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；pH 7.40, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K
Resolution 2.70 Å

25 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PURR_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–289； UniProt 52–340 Author chain B； PDBConstruct 1–289； UniProt 52–340

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 1dbq

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1dbq
Deposition date deposition_date1996-02-13
Structure title titleDNA-BINDING REGULATORY PROTEIN
Keywords keywordsTRANSCRIPTION REGULATION, DNA-BINDING REGULATORY PROTEIN, PURINE REPRESSOR; DNA-BINDING REGULATORY PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier26.88 Å
Radius of gyration Rg (electron density) rg_electron25.86 Å
Forward intensity I(0) i065164800.00
Molecular weight molecular_weight62060.0 kDa
Excluded volume excluded_volume77327 ų
Envelope volume envelope_volume94020 ų
Hydration-shell volume shell_volume30094 ų
Envelope diameter envelope_diameter84.3 Å
Shell Rg shell_rg33.45 Å
Envelope Rg envelope_rg25.93 Å
Shape Rg shape_rg25.87 Å
Total Rg total_rg26.67 Å
Total atoms total_atoms4347
Residues n_residues552
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 dmax82.6 Å
Rg (real space) rg_real26.78 Å
Rg uncertainty (real space) rg_real_error0.54 Å
I(0) (real space) i0_real6.5160e+07
I(0) uncertainty (real space) i0_real_error1.0130e+06
Rg (reciprocal space) rg_reciprocal26.82 Å
I(0) (reciprocal space) i0_reciprocal65170000.0000
Solution quality estimate total_estimate0.9081
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.4 Å
Skewness Skewness skewness0.185
Kurtosis Kurtosis kurtosis-0.561
Angular range angular_range— – 0.2950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha29490000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.957; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.930
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1dbqa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.93 — Periplasmic binding protein-like I
Superfamily Superfamily superfamilyc.93.1 — Periplasmic binding protein-like I
Family Family familyc.93.1.1 — L-arabinose binding protein-like
Domain ID domain_idd1dbqb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.93 — Periplasmic binding protein-like I
Superfamily Superfamily superfamilyc.93.1 — Periplasmic binding protein-like I
Family Family familyc.93.1.1 — L-arabinose binding protein-like

CATH v4.4 (4 domains)

Domain ID domain_id1dbqA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id1dbqA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id1dbqB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id1dbqB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
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8. Citations (1)

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9. Files and Curves (10)