SAXSdb — 1j2a

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

cyclophilin B

Escherichia coli

UniProt P20752

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 25–190	Mutation：K163T	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 1.80 Å R-free 0.225

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 1J2A	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CLH THREE-DIMENSIONAL SOLUTION STRUCTURE OF ESCHERICHIA COLI PERIPLASMIC CYCLOPHILIN Deposited 1993-12-20	Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–190（166 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1V9T Structure of E. coli cyclophilin B K163T mutant bound to succinyl-ALA-PRO-ALA-P-nitroanilide Deposited 2004-02-03	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–166（166 aa）	Mutation：K163T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, methanol, sodium azide, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.221
1V9T Structure of E. coli cyclophilin B K163T mutant bound to succinyl-ALA-PRO-ALA-P-nitroanilide Deposited 2004-02-03	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–166（166 aa）	Mutation：K163T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, methanol, sodium azide, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.221
1VAI Structure of e. coli cyclophilin B K163T mutant bound to n-acetyl-ala-ala-pro-ala-7-amino-4-methylcoumarin Deposited 2004-02-17	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–190（166 aa）	Mutation：K163T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；AMMONIUM SULPHATE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.229
1VAI Structure of e. coli cyclophilin B K163T mutant bound to n-acetyl-ala-ala-pro-ala-7-amino-4-methylcoumarin Deposited 2004-02-17	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 25–190（166 aa）	Mutation：K163T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；AMMONIUM SULPHATE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.229

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PPIA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–166； UniProt 25–190

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	1j2a
Deposition date deposition_date	2002-12-26
Structure title title	Structure of E. coli cyclophilin B K163T mutant
Keywords keywords	BETA BARREL, isomerase; ISOMERASE
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	16.08 Å
Radius of gyration Rg (electron density) rg_electron	14.78 Å
Forward intensity I(0) i0	6347940.00
Molecular weight molecular_weight	18050.0 kDa
Excluded volume excluded_volume	22537 Å³
Envelope volume envelope_volume	25596 Å³
Hydration-shell volume shell_volume	14341 Å³
Envelope diameter envelope_diameter	49.8 Å
Shell Rg shell_rg	20.98 Å
Envelope Rg envelope_rg	15.20 Å
Shape Rg shape_rg	14.76 Å
Total Rg total_rg	16.00 Å
Total atoms total_atoms	1273
Residues n_residues	166
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	54.0 Å
Rg (real space) rg_real	15.95 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	6.3480e+06
I(0) uncertainty (real space) i0_real_error	7.3750e+04
Rg (reciprocal space) rg_reciprocal	15.97 Å
I(0) (reciprocal space) i0_reciprocal	6348000.0000
Solution quality estimate total_estimate	0.7894
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.2 Å
Skewness Skewness skewness	0.081
Kurtosis Kurtosis kurtosis	-0.391
Angular range angular_range	— – 0.4950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1266000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.753; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1j2aa_
Class class	b — All beta proteins
Fold Fold fold	b.62 — Cyclophilin-like
Superfamily Superfamily superfamily	b.62.1 — Cyclophilin-like
Family Family family	b.62.1.1 — Cyclophilin (peptidylprolyl isomerase)

CATH v4.4 (1 domains)

Domain ID domain_id	1j2aA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	100 — Cyclophilin
Homologous superfamily homologous superfamily	10 — Cyclophilin-like

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8. Citations (1)

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Unit-cell length a length_a	82.550 Å
Unit-cell length b length_b	82.550 Å
Unit-cell length c length_c	52.350 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.2010
R_free r_free	0.2250

Description description	cyclophilin B
Molecular weight formula_weight	18070.3 kDa
EC 编号 ec_number	5.2.1.8
Mutation mutation	K163T
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1354

Structure of E. coli cyclophilin B K163T mutant

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

cyclophilin B

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

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)

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	81

fit	/app/data/saxs_computation/j2/1j2a/1j2a.fit
pddf	/app/data/pr_computation/j2/1j2a/1j2a.pr.out
profile	/app/data/saxs_computation/j2/1j2a/1j2a.dat