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1clh

THREE-DIMENSIONAL SOLUTION STRUCTURE OF ESCHERICHIA COLI PERIPLASMIC CYCLOPHILIN

Method: SOLUTION NMR Dmax: 50.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CYCLOPHILIN

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 Not recorded No other associated polymer SOLUTION NMR mmCIF provides none of the parsed experimental conditions 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 1CLH Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1J2A Structure of E. coli cyclophilin B K163T mutant Deposited 2002-12-26 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）
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, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 1.80 Å R-free 0.225
1V9T Structure of E. coli cyclophilin B K163T mutant bound to succinyl-ALA-PRO-ALA-P-nitroanilide Deposited 2004-02-03 Different construct 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 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 mutation/modification Different oligomeric state Different experimental method 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 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）
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 mutation/modification Different oligomeric state Different experimental method 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.

SAXS scattering curve SAXS Profile

SAXS profile for 1clh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1clh
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1clh
Deposition date deposition_date1993-12-20
Structure title titleTHREE-DIMENSIONAL SOLUTION STRUCTURE OF ESCHERICHIA COLI PERIPLASMIC CYCLOPHILIN
Keywords keywordsISOMERASE(PEPTIDYL-PROLYL CIS-TRANS); ISOMERASE(PEPTIDYL-PROLYL CIS-TRANS)
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.41 Å
Radius of gyration Rg (electron density) rg_electron15.06 Å
Forward intensity I(0) i0664801000.00
Molecular weight molecular_weight216940.0 kDa
Excluded volume excluded_volume271120 ų
Envelope volume envelope_volume39094 ų
Hydration-shell volume shell_volume18723 ų
Envelope diameter envelope_diameter55.4 Å
Shell Rg shell_rg23.80 Å
Envelope Rg envelope_rg17.37 Å
Shape Rg shape_rg15.03 Å
Total Rg total_rg15.36 Å
Total atoms total_atoms30420
Residues n_residues1992
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax50.0 Å
Rg (real space) rg_real15.29 Å
Rg uncertainty (real space) rg_real_error0.24 Å
I(0) (real space) i0_real6.6480e+08
I(0) uncertainty (real space) i0_real_error6.6100e+06
Rg (reciprocal space) rg_reciprocal15.30 Å
I(0) (reciprocal space) i0_reciprocal664800000.0000
Solution quality estimate total_estimate0.8722
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary48.7 Å
Skewness Skewness skewness0.007
Kurtosis Kurtosis kurtosis-0.439
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha753400.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.784; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.990
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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_idd1clha_
Class classb — All beta proteins
Fold Fold foldb.62 — Cyclophilin-like
Superfamily Superfamily superfamilyb.62.1 — Cyclophilin-like
Family Family familyb.62.1.1 — Cyclophilin (peptidylprolyl isomerase)

CATH v4.4 (1 domains)

Domain ID domain_id1clhA00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology100 — Cyclophilin
Homologous superfamily homologous superfamily10 — Cyclophilin-like
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8. Citations (1)

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9. Files and Curves (10)