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1urp

D-RIBOSE-BINDING PROTEIN FROM ESCHERICHIA COLI

Method: X-RAY DIFFRACTION Dmax: 123.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

D-RIBOSE-BINDING PROTEIN

Escherichia coli K12

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 No other associated polymer 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 26–296 Not recorded No other associated polymer 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
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 26–296 Not recorded No other associated polymer 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
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain D； UniProt 26–296 Not recorded No other associated polymer 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

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 1URP 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 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 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
1DBP IDENTICAL MUTATIONS AT CORRESPONDING POSITIONS IN TWO HOMOLOGOUS PROTEINS WITH NON-IDENTICAL EFFECTS Deposited 1994-01-31 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 RIP beta-D-ribopyranose × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å
1DRJ PROBING PROTEIN-PROTEIN INTERACTIONS: THE RIBOSE-BINDING PROTEIN IN BACTERIAL TRANSPORT AND CHEMOTAXIS Deposited 1994-09-23 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 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 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 RIP beta-D-ribopyranose × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
2DRI PROBING PROTEIN-PROTEIN INTERACTIONS: THE RIBOSE BINDING PROTEIN IN BACTERIAL TRANSPORT AND CHEMOTAXIS Deposited 1994-09-23 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 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 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：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 7 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 Author chain B； PDBConstruct 1–271； UniProt 26–296 Author chain C； PDBConstruct 1–271； UniProt 26–296 Author chain D； 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 1urp

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1urp
Deposition date deposition_date1998-04-03
Structure title titleD-RIBOSE-BINDING PROTEIN FROM ESCHERICHIA COLI
Keywords keywordsTRANSPORT, CHEMOTAXIS, PERIPLASM; TRANSPORT
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_guinier40.46 Å
Radius of gyration Rg (electron density) rg_electron40.50 Å
Forward intensity I(0) i0196448000.00
Molecular weight molecular_weight113890.0 kDa
Excluded volume excluded_volume143020 ų
Envelope volume envelope_volume200970 ų
Hydration-shell volume shell_volume43700 ų
Envelope diameter envelope_diameter130.4 Å
Shell Rg shell_rg43.40 Å
Envelope Rg envelope_rg39.63 Å
Shape Rg shape_rg40.48 Å
Total Rg total_rg40.77 Å
Total atoms total_atoms8008
Residues n_residues1084
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 dmax123.5 Å
Rg (real space) rg_real40.43 Å
Rg uncertainty (real space) rg_real_error0.96 Å
I(0) (real space) i0_real1.9640e+08
I(0) uncertainty (real space) i0_real_error3.1460e+06
Rg (reciprocal space) rg_reciprocal40.46 Å
I(0) (reciprocal space) i0_reciprocal196500000.0000
Solution quality estimate total_estimate0.8643
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary47.5 Å
Skewness Skewness skewness0.148
Kurtosis Kurtosis kurtosis-0.741
Angular range angular_range— – 0.1950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8793000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.978; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.335
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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) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1urpa_
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_idd1urpb_
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_idd1urpc_
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_idd1urpd_
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 (8 domains)

Domain ID domain_id1urpA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id1urpA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id1urpB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id1urpB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id1urpC01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id1urpC02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id1urpD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id1urpD02
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 (5)

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9. Files and Curves (10)