SAXSdb — 1drj

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1. Protein Identity and Related Structures Protein Identity & Related Structures

D-RIBOSE-BINDING PROTEIN

Escherichia coli

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 2.50 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 1DRJ	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
1DBP IDENTICAL MUTATIONS AT CORRESPONDING POSITIONS IN TWO HOMOLOGOUS PROTEINS WITH NON-IDENTICAL EFFECTS Deposited 1994-01-31	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
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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1drj
Deposition date deposition_date	1994-09-23
Structure title title	PROBING PROTEIN-PROTEIN INTERACTIONS: THE RIBOSE-BINDING PROTEIN IN BACTERIAL TRANSPORT AND CHEMOTAXIS
Keywords keywords	SUGAR TRANSPORT; SUGAR TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	19.98 Å
Radius of gyration Rg (electron density) rg_electron	19.25 Å
Forward intensity I(0) i0	14705600.00
Molecular weight molecular_weight	28723.0 kDa
Excluded volume excluded_volume	36059 Å³
Envelope volume envelope_volume	41426 Å³
Hydration-shell volume shell_volume	18411 Å³
Envelope diameter envelope_diameter	64.8 Å
Shell Rg shell_rg	25.04 Å
Envelope Rg envelope_rg	19.57 Å
Shape Rg shape_rg	19.21 Å
Total Rg total_rg	20.20 Å
Total atoms total_atoms	2497
Residues n_residues	271
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	63.9 Å
Rg (real space) rg_real	20.02 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	1.4710e+07
I(0) uncertainty (real space) i0_real_error	1.9740e+05
Rg (reciprocal space) rg_reciprocal	20.01 Å
I(0) (reciprocal space) i0_reciprocal	14710000.0000
Solution quality estimate total_estimate	0.8061
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.4 Å
Skewness Skewness skewness	0.433
Kurtosis Kurtosis kurtosis	-0.269
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4989000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.832; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; 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)

Entity 1 Entity 1 polymer

Description description	D-RIBOSE-BINDING PROTEIN
Molecular weight formula_weight	28607.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2938

KDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQATKGEVVSHIASDNVLGGKIAGDYIAKKAGEGAKVIELQGIARTSAARERGEGFQQAVAAHKFNVLASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGKSDVMVVGFDGTPDGEKAVNDGKLAATIAQLPDQIGAKGVETADKVLKGEKVQAKYPVDLKLVVKQ

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562

Entity 2 Entity 2 non-polymer

Description description	beta-D-ribopyranose
Molecular weight formula_weight	150.1 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	147

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1drja_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.93 — Periplasmic binding protein-like I
Superfamily Superfamily superfamily	c.93.1 — Periplasmic binding protein-like I
Family Family family	c.93.1.1 — L-arabinose binding protein-like

CATH v4.4 (2 domains)

Domain ID domain_id	1drjA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	1drjA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

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8. Citations (4)

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Unit-cell length a length_a	74.910 Å
Unit-cell length b length_b	90.080 Å
Unit-cell length c length_c	39.280 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	7.500 Å
R factor r_factor	0.1760
R_work r_work	0.1760
R_free r_free	—

fit	/app/data/saxs_computation/dr/1drj/1drj.fit
pddf	/app/data/pr_computation/dr/1drj/1drj.pr.out
profile	/app/data/saxs_computation/dr/1drj/1drj.dat

PROBING PROTEIN-PROTEIN INTERACTIONS: THE RIBOSE-BINDING PROTEIN IN BACTERIAL TRANSPORT AND CHEMOTAXIS

1. Protein Identity and Related Structures Protein Identity & Related Structures

D-RIBOSE-BINDING PROTEIN

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution