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1dbp

IDENTICAL MUTATIONS AT CORRESPONDING POSITIONS IN TWO HOMOLOGOUS PROTEINS WITH NON-IDENTICAL EFFECTS

Method: X-RAY DIFFRACTION Dmax: 64.6 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

D-RIBOSE-BINDING PROTEIN

Escherichia coli

UniProt P02925

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 26–296 Not recorded RIP beta-D-ribopyranose × 1 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 1DBP Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BA2 D67R MUTANT OF D-RIBOSE-BINDING PROTEIN FROM ESCHERICHIA COLI Deposited 1998-04-19 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–296（271 aa）
Mutation：D67R No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；VAPOR DIFFUSION OF DROPS CONTAINING 7.5 MG/ML PROTEIN AGAINST A RESERVOIR OF 24% PEG4000, 100 MM TRIS-HCL, PH 7., pH 7.0, vapor diffusion
Resolution 2.10 Å R-free 0.279
1BA2 D67R MUTANT OF D-RIBOSE-BINDING PROTEIN FROM ESCHERICHIA COLI Deposited 1998-04-19 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 26–296（271 aa）
Mutation：D67R No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；VAPOR DIFFUSION OF DROPS CONTAINING 7.5 MG/ML PROTEIN AGAINST A RESERVOIR OF 24% PEG4000, 100 MM TRIS-HCL, PH 7., pH 7.0, vapor diffusion
Resolution 2.10 Å R-free 0.279
1DRJ PROBING PROTEIN-PROTEIN INTERACTIONS: THE RIBOSE-BINDING PROTEIN IN BACTERIAL TRANSPORT AND CHEMOTAXIS Deposited 1994-09-23 Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–296（271 aa）
Not recorded RIP beta-D-ribopyranose × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
1DRK PROBING PROTEIN-PROTEIN INTERACTIONS: THE RIBOSE-BINDING PROTEIN IN BACTERIAL TRANSPORT AND CHEMOTAXIS Deposited 1994-09-23 Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–296（271 aa）
Not recorded RIP beta-D-ribopyranose × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
1URP D-RIBOSE-BINDING PROTEIN FROM ESCHERICHIA COLI Deposited 1998-04-03 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–296（271 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；CRYSTALS WERE OBTAINED FROM SOLUTIONS OF 7.5 - 15 MG/ML RBP, 21% PEG4000, 50-100 MM SODIUM CITRATE, PH 4, 5% GLYCEROL, BY HANGING DROP VAPOUR DIFFUSION., pH 5.0, vapor diffusion - hanging drop
Resolution 2.30 Å R-free 0.267
1URP D-RIBOSE-BINDING PROTEIN FROM ESCHERICHIA COLI Deposited 1998-04-03 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 26–296（271 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；CRYSTALS WERE OBTAINED FROM SOLUTIONS OF 7.5 - 15 MG/ML RBP, 21% PEG4000, 50-100 MM SODIUM CITRATE, PH 4, 5% GLYCEROL, BY HANGING DROP VAPOUR DIFFUSION., pH 5.0, vapor diffusion - hanging drop
Resolution 2.30 Å R-free 0.267
1URP D-RIBOSE-BINDING PROTEIN FROM ESCHERICHIA COLI Deposited 1998-04-03 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 26–296（271 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；CRYSTALS WERE OBTAINED FROM SOLUTIONS OF 7.5 - 15 MG/ML RBP, 21% PEG4000, 50-100 MM SODIUM CITRATE, PH 4, 5% GLYCEROL, BY HANGING DROP VAPOUR DIFFUSION., pH 5.0, vapor diffusion - hanging drop
Resolution 2.30 Å R-free 0.267
1URP D-RIBOSE-BINDING PROTEIN FROM ESCHERICHIA COLI Deposited 1998-04-03 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 26–296（271 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；CRYSTALS WERE OBTAINED FROM SOLUTIONS OF 7.5 - 15 MG/ML RBP, 21% PEG4000, 50-100 MM SODIUM CITRATE, PH 4, 5% GLYCEROL, BY HANGING DROP VAPOUR DIFFUSION., pH 5.0, vapor diffusion - hanging drop
Resolution 2.30 Å R-free 0.267
2DRI PROBING PROTEIN-PROTEIN INTERACTIONS: THE RIBOSE BINDING PROTEIN IN BACTERIAL TRANSPORT AND CHEMOTAXIS Deposited 1994-09-23 Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–296（271 aa）
Not recorded RIP beta-D-ribopyranose × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.60 Å
2GX6 Rational stabilization of E. coli ribose binding protein Deposited 2006-05-08 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–296（271 aa）
Mutation：T83V,T91V,T272V RIP beta-D-ribopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；290 K；36% PEG4000, 0.1M NaAcetate pH5.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 1.97 Å R-free 0.229

6 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RBSB_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–271； UniProt 26–296

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 1dbp

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1dbp
Deposition date deposition_date1994-01-31
Structure title titleIDENTICAL MUTATIONS AT CORRESPONDING POSITIONS IN TWO HOMOLOGOUS PROTEINS WITH NON-IDENTICAL EFFECTS
Keywords keywordsBINDING PROTEIN; BINDING 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_guinier19.91 Å
Radius of gyration Rg (electron density) rg_electron19.22 Å
Forward intensity I(0) i014583500.00
Molecular weight molecular_weight28680.0 kDa
Excluded volume excluded_volume35991 ų
Envelope volume envelope_volume40999 ų
Hydration-shell volume shell_volume18287 ų
Envelope diameter envelope_diameter64.4 Å
Shell Rg shell_rg24.95 Å
Envelope Rg envelope_rg19.51 Å
Shape Rg shape_rg19.19 Å
Total Rg total_rg20.13 Å
Total atoms total_atoms2489
Residues n_residues271
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 dmax64.6 Å
Rg (real space) rg_real19.95 Å
Rg uncertainty (real space) rg_real_error0.44 Å
I(0) (real space) i0_real1.4580e+07
I(0) uncertainty (real space) i0_real_error1.6570e+05
Rg (reciprocal space) rg_reciprocal19.95 Å
I(0) (reciprocal space) i0_reciprocal14580000.0000
Solution quality estimate total_estimate0.6478
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.8 Å
Skewness Skewness skewness0.435
Kurtosis Kurtosis kurtosis-0.273
Angular range angular_range— – 0.4000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4821000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.811; Stabil: 0.999; Sysdev: 0.338; Positv: 1.000; Valcen: 0.974; Smooth: 0.000
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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) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1dbpa_
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 (2 domains)

Domain ID domain_id1dbpA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id1dbpA02
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 (4)

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9. Files and Curves (10)