2zr4

Crystal structure of a mutant PIN1 peptidyl-prolyl cis-trans isomerase

Method: X-RAY DIFFRACTION Dmax: 58.0 Å Quality: GOOD

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

Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1

Homo sapiens

UniProt Q13526

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 1–163 Mutation:S32A 1PG 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;278 K;2.5M ammonium sulfate, 100mM HEPES-NA(pH7.5), 2% PEG400, 2mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 278K Resolution 2.00 Å R-free 0.266

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.

189 other PDB entries and 218 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PIN1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–163; UniProt 1–163

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 2zr4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2zr4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2zr4
Deposition date deposition_date2008-08-22
Structure title titleCrystal structure of a mutant PIN1 peptidyl-prolyl cis-trans isomerase
Keywords keywordsPIN1 mutant (S32A), ISOMERASE, Cell cycle, Nucleus, Phosphoprotein, Rotamase; ISOMERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier17.05
Radius of gyration Rg (electron density) rg_electron15.89
Forward intensity I(0) i06473660.00
Molecular weight molecular_weight17557.0 kDa
Excluded volume excluded_volume21590 ų
Envelope volume envelope_volume25441 ų
Hydration-shell volume shell_volume13741 ų
Envelope diameter envelope_diameter58.7
Shell Rg shell_rg21.42
Envelope Rg envelope_rg16.33
Shape Rg shape_rg15.86
Total Rg total_rg16.92
Total atoms total_atoms1233
Residues n_residues153
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax58.0
Rg (real space) rg_real16.99
Rg uncertainty (real space) rg_real_error0.38
I(0) (real space) i0_real6.4740e+06
I(0) uncertainty (real space) i0_real_error7.5470e+04
Rg (reciprocal space) rg_reciprocal17.00
I(0) (reciprocal space) i0_reciprocal6474000.0000
Solution quality estimate total_estimate0.7998
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary21.4
Skewness Skewness skewness0.236
Kurtosis Kurtosis kurtosis-0.334
Angular range angular_range— – 0.4650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1174000.0000
Real-space data points n_real_points77
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.806; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2zr4a1
Class classb — All beta proteins
Fold Fold foldb.72 — WW domain-like
Superfamily Superfamily superfamilyb.72.1 — WW domain
Family Family familyb.72.1.1 — WW domain
Domain ID domain_idd2zr4a2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.26 — FKBP-like
Superfamily Superfamily superfamilyd.26.1 — FKBP-like
Family Family familyd.26.1.1 — FKBP immunophilin/proline isomerase

CATH v4.4 (2 domains)

Domain ID domain_id2zr4A01
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology70 — Ubiquitin Ligase Nedd4; Chain: W;
Homologous superfamily homologous superfamily10
Domain ID domain_id2zr4A02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily40

8. Citations (1)

9. Files and Curves (10)