SAXSdb — 2f52

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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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–67	Not recorded	No other associated polymer	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

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 2F52	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 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	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 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	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 experimental conditions	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 experimental conditions	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 method 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
2I5L Crystal structure of Bacillus subtilis Cold Shock Protein variant Bs-CspB M1R/E3K/K65I Deposited 2006-08-25	Different mutation/modification Different experimental method 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 ligand/ion Different experimental method 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 method 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 ligand/ion 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	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 oligomeric state Different experimental method 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
3PF5 Crystal structure of Bs-CspB in complex with rU6 Deposited 2010-10-27	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–67（67 aa）	Not recorded	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
3PF5 Crystal structure of Bs-CspB in complex with rU6 Deposited 2010-10-27	Different oligomeric state Different experimental method 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.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

9 other PDB entries and 12 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

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	2f52
Deposition date deposition_date	2005-11-25
Structure title title	Solution structure of cold shock protein CspB from Bacillus subtilis in complex with heptathymidine
Keywords keywords	beta barrel, OB-fold, DNA BINDING PROTEIN-TRANSCRIPTION COMPLEX; DNA BINDING PROTEIN/TRANSCRIPTION
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	11.30 Å
Radius of gyration Rg (electron density) rg_electron	10.87 Å
Forward intensity I(0) i0	248248000.00
Molecular weight molecular_weight	132460.0 kDa
Excluded volume excluded_volume	165050 Å³
Envelope volume envelope_volume	14255 Å³
Hydration-shell volume shell_volume	10004 Å³
Envelope diameter envelope_diameter	40.6 Å
Shell Rg shell_rg	17.86 Å
Envelope Rg envelope_rg	12.63 Å
Shape Rg shape_rg	10.84 Å
Total Rg total_rg	11.16 Å
Total atoms total_atoms	18252
Residues n_residues	1206
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	37.0 Å
Rg (real space) rg_real	11.23 Å
Rg uncertainty (real space) rg_real_error	0.29 Å
I(0) (real space) i0_real	2.4820e+08
I(0) uncertainty (real space) i0_real_error	2.4940e+06
Rg (reciprocal space) rg_reciprocal	11.24 Å
I(0) (reciprocal space) i0_reciprocal	248200000.0000
Solution quality estimate total_estimate	0.7911
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	15.0 Å
Skewness Skewness skewness	0.099
Kurtosis Kurtosis kurtosis	-0.246
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	114300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.764; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2f52a_
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 (1 domains)

Domain ID domain_id	2f52A00
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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Description description	Cold shock protein cspB
Molecular weight formula_weight	7372.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	18252

来源生物 organism	Bacillus subtilis
NCBI Class编号 ncbi_taxonomy_id	1423
宿主生物 host_organism	Escherichia coli BL21(DE3)

fit	/app/data/saxs_computation/f5/2f52/2f52.fit
pddf	/app/data/pr_computation/f5/2f52/2f52.pr.out
profile	/app/data/saxs_computation/f5/2f52/2f52.dat

Solution structure of cold shock protein CspB from Bacillus subtilis in complex with heptathymidine

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)