SAXSdb — 1hzc

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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：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

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 1HZC	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 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
1I5F BACILLUS CALDOLYTICUS COLD-SHOCK PROTEIN MUTANTS TO STUDY DETERMINANTS OF PROTEIN STABILITY Deposited 2001-02-27	Different mutation/modification 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
5JX4 Crystal structure of E36-G37del mutant of the Bacillus caldolyticus cold shock protein. Deposited 2016-05-12	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：E36del, G37del 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

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 1–66； UniProt 1–66 Author chain B； PDBConstruct 1–66； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1hzc
Deposition date deposition_date	2001-01-24
Structure title title	BACILLUS CALDOLYTICUS COLD-SHOCK PROTEIN MUTANTS TO STUDY DETERMINANTS OF PROTEIN STABILITY
Keywords keywords	BETA BARREL, HOMODIMER, TRANSCRIPTION; TRANSCRIPTION
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	16.24 Å
Radius of gyration Rg (electron density) rg_electron	15.12 Å
Forward intensity I(0) i0	4254340.00
Molecular weight molecular_weight	14543.0 kDa
Excluded volume excluded_volume	18121 Å³
Envelope volume envelope_volume	21610 Å³
Hydration-shell volume shell_volume	12469 Å³
Envelope diameter envelope_diameter	51.4 Å
Shell Rg shell_rg	20.36 Å
Envelope Rg envelope_rg	15.30 Å
Shape Rg shape_rg	15.12 Å
Total Rg total_rg	16.18 Å
Total atoms total_atoms	1029
Residues n_residues	132
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	52.4 Å
Rg (real space) rg_real	16.20 Å
Rg uncertainty (real space) rg_real_error	0.26 Å
I(0) (real space) i0_real	4.2540e+06
I(0) uncertainty (real space) i0_real_error	4.6270e+04
Rg (reciprocal space) rg_reciprocal	16.20 Å
I(0) (reciprocal space) i0_reciprocal	4254000.0000
Solution quality estimate total_estimate	0.8830
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.5 Å
Skewness Skewness skewness	0.286
Kurtosis Kurtosis kurtosis	-0.341
Angular range angular_range	— – 0.4900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1300000.0000
Real-space data points n_real_points	79
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.842; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.949

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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	COLD SHOCK PROTEIN CSPB
Molecular weight formula_weight	7271.0 kDa
Mutation mutation	R3E,E46A,L66E
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	1368

MQEGKVKWFNNEKGYGFIEVEGGSDVFVHFTAIQGEGFKTLEEGQAVSFEIVQGNRGPQAANVVKE

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	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
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	270

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1hzca_
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	d1hzcb_
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	1hzcA00
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	1hzcB00
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	76.864 Å
Unit-cell length b length_b	76.864 Å
Unit-cell length c length_c	48.024 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	16

Space group space_group	I 41
Space-group number int_tables_number	80
Crystal system crystal_system	—

Resolution resolution	1.320 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1440
R_work r_work	0.1390
R_free r_free	0.1810

fit	/app/data/saxs_computation/hz/1hzc/1hzc.fit
pddf	/app/data/pr_computation/hz/1hzc/1hzc.pr.out
profile	/app/data/saxs_computation/hz/1hzc/1hzc.dat

BACILLUS CALDOLYTICUS COLD-SHOCK PROTEIN MUTANTS TO STUDY DETERMINANTS OF PROTEIN STABILITY

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