SAXSdb — 3pf5

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

Cold shock protein cspB

Bacillus subtilis

UniProt P32081

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–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain A； UniProt 1–67	Not recorded	hexaribouracil (rU6) × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；protein buffer: 50mM TRIS, 20mM Na-HEPES, pH 7.5; Bs-CspB.rU6 complex concentration: 70mg/ml; crystallization buffer: 31% PEG 3350, 0.25M MgCl2, 0.1M TRIS pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 1.68 Å R-free 0.235
2	Protein–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain B； UniProt 1–67	Not recorded	hexaribouracil (rU6) × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；protein buffer: 50mM TRIS, 20mM Na-HEPES, pH 7.5; Bs-CspB.rU6 complex concentration: 70mg/ml; crystallization buffer: 31% PEG 3350, 0.25M MgCl2, 0.1M TRIS pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 1.68 Å R-free 0.235

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 3PF5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CSP CRYSTAL STRUCTURE OF THE BACILLUS SUBTILIS MAJOR COLD SHOCK PROTEIN, CSPB: A UNIVERSAL NUCLEIC-ACID BINDING DOMAIN Deposited 1993-05-12	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–67（67 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.45 Å
1CSQ CRYSTAL STRUCTURE OF THE BACILLUS SUBTILIS MAJOR COLD SHOCK PROTEIN, CSPB: A UNIVERSAL NUCLEIC-ACID BINDING DOMAIN Deposited 1993-05-12	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–67（67 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.70 Å
1NMF MAJOR COLD-SHOCK PROTEIN, NMR, 20 STRUCTURES Deposited 1996-02-05	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–67（67 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1NMG MAJOR COLD-SHOCK PROTEIN, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1996-02-05	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–67（67 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
2ES2 Crystal Structure Analysis of the Bacillus Subtilis Cold Shock Protein Bs-CspB in Complex with Hexathymidine Deposited 2005-10-25	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–67（67 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2M calcium acetate 18% (w/v) PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.78 Å R-free 0.223
2F52 Solution structure of cold shock protein CspB from Bacillus subtilis in complex with heptathymidine Deposited 2005-11-25	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–67（67 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；288 K；Ionic strength (raw mmCIF value) 53mM buffer salt；Pressure ambient NMR sample composition 0.8mM CspB U-15N, 50mM Na-cacodylate, 3mM MgCl2, 1.2mM heptathymidine, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.8mM CspB U-15N, 13C, 50mM Na-cacodylate, 3mM MgCl2, 1.2mM heptathymidine, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2I5L Crystal structure of Bacillus subtilis Cold Shock Protein variant Bs-CspB M1R/E3K/K65I Deposited 2006-08-25	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 1–67（67 aa）	Mutation：M1R, E3K, K65I	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；protein solution: 20 mM TRIS pH 7.5, 50 mM sodium chloride, 3 mM magnesium chloride, 20.4 mg/ml protein. crystallization buffer: 25 % PEG 3350, 0.2 M sodium carbonate, 0.1 M TRIS HCl pH 8.5. crystallization setup: 0.8 microliter protein solution:0.8 microliter reservoir solution, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.55 Å R-free 0.244
2I5M Crystal structure of Bacillus subtilis cold shock protein CspB variant A46K S48R Deposited 2006-08-25	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 1–67（67 aa）	Mutation：A46K, S48R	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；reservoir solution: 1.5 M lithium sulfate, 0.1 M TRIS pH 7.5, 15% glycerol for cryoprotection. protein solution: 20 mM TRIS pH 7.5, 50 mM NaCl, 3 mM MgCl2, 17.4 mg/ml protein. crystallization setup: 0.8 microliter protein solution:0.8 microliter reservoir solution, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.30 Å R-free 0.227
2I5M Crystal structure of Bacillus subtilis cold shock protein CspB variant A46K S48R Deposited 2006-08-25	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain X 1–67（67 aa）	Mutation：A46K, S48R	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；reservoir solution: 1.5 M lithium sulfate, 0.1 M TRIS pH 7.5, 15% glycerol for cryoprotection. protein solution: 20 mM TRIS pH 7.5, 50 mM NaCl, 3 mM MgCl2, 17.4 mg/ml protein. crystallization setup: 0.8 microliter protein solution:0.8 microliter reservoir solution, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.30 Å R-free 0.227
3PF4 Crystal structure of Bs-CspB in complex with r(GUCUUUA) Deposited 2010-10-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–67（67 aa）	Not recorded	NA SODIUM ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；protein buffer: 50mM TRIS, 20mM Na-HEPES, pH 7.5; Bs-CspB.rGUCUUUA complex concentration: 50mg/ml; crystallization buffer: 30% (w/v) PEG 4000, 0.2M MgCl2, 0.1M TRIS pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 1.38 Å R-free 0.194
3PF4 Crystal structure of Bs-CspB in complex with r(GUCUUUA) Deposited 2010-10-27	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–67（67 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；protein buffer: 50mM TRIS, 20mM Na-HEPES, pH 7.5; Bs-CspB.rGUCUUUA complex concentration: 50mg/ml; crystallization buffer: 30% (w/v) PEG 4000, 0.2M MgCl2, 0.1M TRIS pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 1.38 Å R-free 0.194

9 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CSPB_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–67； UniProt 1–67 Author chain B； PDBConstruct 1–67； UniProt 1–67

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	3pf5
Deposition date deposition_date	2010-10-27
Structure title title	Crystal structure of Bs-CspB in complex with rU6
Keywords keywords	;BETA BARREL, PROTEIN-RNA complex, COLD SHOCK RESPONSE, TRANSCRIPTION REGULATION, TRANSLATION REGULATION, OB fold, cold shock domain, RNA/DNA binding, single-stranded RNA and DNA, cytosol, GENE REGULATION-RNA complex ;; GENE REGULATION/RNA
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	18.27 Å
Radius of gyration Rg (electron density) rg_electron	17.35 Å
Forward intensity I(0) i0	5839120.00
Molecular weight molecular_weight	16434.0 kDa
Excluded volume excluded_volume	19994 Å³
Envelope volume envelope_volume	24851 Å³
Hydration-shell volume shell_volume	12700 Å³
Envelope diameter envelope_diameter	60.1 Å
Shell Rg shell_rg	22.06 Å
Envelope Rg envelope_rg	17.39 Å
Shape Rg shape_rg	17.33 Å
Total Rg total_rg	18.19 Å
Total atoms total_atoms	1154
Residues n_residues	139
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	60.7 Å
Rg (real space) rg_real	18.30 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	5.8390e+06
I(0) uncertainty (real space) i0_real_error	7.2380e+04
Rg (reciprocal space) rg_reciprocal	18.29 Å
I(0) (reciprocal space) i0_reciprocal	5839000.0000
Solution quality estimate total_estimate	0.8771
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	59.0 Å
Skewness Skewness skewness	0.347
Kurtosis Kurtosis kurtosis	-0.490
Angular range angular_range	— – 0.4350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1918000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.816; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.952; Smooth: 0.998

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Cold shock protein cspB
Molecular weight formula_weight	7372.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1359

MLEGKVKWFNSEKGFGFIEVEGQDDVFVHFSAIQGEGFKTLEEGQAVSFEIVEGNRGPQAANVTKEA

来源 Source

来源生物 organism	Bacillus subtilis
NCBI Class编号 ncbi_taxonomy_id	1423
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	hexaribouracil (rU6)
Molecular weight formula_weight	1792.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	R,S

UUUUUU

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	178

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3pf5a_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.5 — Cold shock DNA-binding domain-like

Domain ID domain_id	d3pf5b_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.5 — Cold shock DNA-binding domain-like

CATH v4.4 (2 domains)

Domain ID domain_id	3pf5A00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	3pf5B00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

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8. Citations (1)

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Unit-cell length a length_a	49.038 Å
Unit-cell length b length_b	49.769 Å
Unit-cell length c length_c	57.380 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	8

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

Resolution resolution	1.680 Å
Low-resolution limit resolution_low	17.460 Å
R factor r_factor	0.1825
R_work r_work	0.1798
R_free r_free	0.2347

fit	/app/data/saxs_computation/pf/3pf5/3pf5.fit
pddf	/app/data/pr_computation/pf/3pf5/3pf5.pr.out
profile	/app/data/saxs_computation/pf/3pf5/3pf5.dat

Crystal structure of Bs-CspB in complex with rU6

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

Cold shock protein cspB

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

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)