SAXSdb — 5jx4

▼

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

Cold shock protein CspB

Bacillus caldolyticus

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–66 Chain B； UniProt 1–66	Mutation：E36del, G37del	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；291 K；0.1 M Sodium Acetate, Poly(ethylene glycol) methyl ether 2000 30%, 0.2 M Ammonium Sulfate. Protein 20 mg/mL in 20 mM Sodium phosphate.	Resolution 1.80 Å R-free 0.182

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 5JX4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C9O CRYSTAL STRUCTURE ANALYSIS OF THE BACILLUS CALDOLYTICUS COLD SHOCK PROTEIN BC-CSP Deposited 1999-08-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–66（66 aa） Chain B 1–66（66 aa）	Not recorded	NA SODIUM ION × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；MPD, HEPES, pH 7.5. VAPOR DIFFUSION, HANGING DROP at 293	Resolution 1.17 Å R-free 0.179
1HZ9 BACILLUS CALDOLYTICUS COLD-SHOCK PROTEIN MUTANTS TO STUDY DETERMINANTS OF PROTEIN STABILITY Deposited 2001-01-24	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–66（66 aa） Chain B 1–66（66 aa）	Mutation：E46A Mutation：E46A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；MPD, Na-Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.80 Å R-free 0.234
1HZA BACILLUS CALDOLYTICUS COLD-SHOCK PROTEIN MUTANTS TO STUDY DETERMINANTS OF PROTEIN STABILITY Deposited 2001-01-24	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–66（66 aa） Chain B 1–66（66 aa）	Mutation：V64T,L66E,67A Mutation：V64T,L66E,67A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；PEG 800, sodium chloride, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.80 Å R-free 0.246
1HZB BACILLUS CALDOLYTICUS COLD-SHOCK PROTEIN MUTANTS TO STUDY DETERMINANTS OF PROTEIN STABILITY Deposited 2001-01-24	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–66（66 aa） Chain B 1–66（66 aa）	Mutation：L66E Mutation：L66E	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；MPD, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.28 Å R-free 0.189
1HZC BACILLUS CALDOLYTICUS COLD-SHOCK PROTEIN MUTANTS TO STUDY DETERMINANTS OF PROTEIN STABILITY Deposited 2001-01-24	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–66（66 aa） Chain B 1–66（66 aa）	Mutation：R3E,E46A,L66E Mutation：R3E,E46A,L66E	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；MPD, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.32 Å R-free 0.181
1I5F BACILLUS CALDOLYTICUS COLD-SHOCK PROTEIN MUTANTS TO STUDY DETERMINANTS OF PROTEIN STABILITY Deposited 2001-02-27	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–66（66 aa） Chain B 1–66（66 aa）	Mutation：R3E Mutation：R3E	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；PEG 6000, sodium citrate, ammonia sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.40 Å R-free 0.205
2HAX Crystal structure of Bacillus caldolyticus cold shock protein in complex with hexathymidine Deposited 2006-06-13	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–66（66 aa） Chain B 1–66（66 aa）	Not recorded	CA CALCIUM ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293.15 K；35% 2-methyl-2,4-pentanediol, 0.1 M sodium acetate pH 4.6, 0.02 M CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 1.29 Å R-free 0.162

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CSPB_BACCL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–66； UniProt 1–66 Author chain B； PDBConstruct 3–66； UniProt 1–66

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5jx4
Deposition date deposition_date	2016-05-12
Structure title title	Crystal structure of E36-G37del mutant of the Bacillus caldolyticus cold shock protein.
Keywords keywords	BcCSP, monomer, mutant, cold shock protein., DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	17.69 Å
Radius of gyration Rg (electron density) rg_electron	16.45 Å
Forward intensity I(0) i0	4923930.00
Molecular weight molecular_weight	15104.0 kDa
Excluded volume excluded_volume	18556 Å³
Envelope volume envelope_volume	23246 Å³
Hydration-shell volume shell_volume	12527 Å³
Envelope diameter envelope_diameter	60.3 Å
Shell Rg shell_rg	21.39 Å
Envelope Rg envelope_rg	16.76 Å
Shape Rg shape_rg	16.34 Å
Total Rg total_rg	17.68 Å
Total atoms total_atoms	1061
Residues n_residues	131
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

▼

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

Maximum dimension Dmax dmax	60.6 Å
Rg (real space) rg_real	17.71 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	4.9240e+06
I(0) uncertainty (real space) i0_real_error	5.8890e+04
Rg (reciprocal space) rg_reciprocal	17.71 Å
I(0) (reciprocal space) i0_reciprocal	4924000.0000
Solution quality estimate total_estimate	0.7813
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	18.6 Å
Skewness Skewness skewness	0.386
Kurtosis Kurtosis kurtosis	-0.299
Angular range angular_range	— – 0.4500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1593000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.750; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.910; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Cold shock protein CspB
Molecular weight formula_weight	7350.2 kDa
Mutation mutation	E36del, G37del
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	1295

GHMQRGKVKWFNNEKGYGFIEVEGGSDVFVHFTAIQGFKTLEEGQEVSFEIVQGNRGPQAANVVKL

来源 Source

来源生物 organism	Bacillus caldolyticus
NCBI Class编号 ncbi_taxonomy_id	1394
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	221

▼

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5jx4a1
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	d5jx4a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5jx4b1
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	d5jx4b2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	5jx4A00
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	5jx4B00
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

▶

8. Citations (1)

▶

Unit-cell length a length_a	34.009 Å
Unit-cell length b length_b	44.077 Å
Unit-cell length c length_c	36.484 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.28 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	18.797 Å
R factor r_factor	0.1515
R_work r_work	0.1500
R_free r_free	0.1821

fit	/app/data/saxs_computation/jx/5jx4/5jx4.fit
pddf	/app/data/pr_computation/jx/5jx4/5jx4.pr.out
profile	/app/data/saxs_computation/jx/5jx4/5jx4.dat

Crystal structure of E36-G37del mutant of the Bacillus caldolyticus cold shock protein.

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