1ddk

CRYSTAL STRUCTURE OF IMP-1 METALLO BETA-LACTAMASE FROM PSEUDOMONAS AERUGINOSA

Method: X-RAY DIFFRACTION Dmax: 57.9 Å Quality: GOOD

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

IMP-1 METALLO BETA-LACTAMASE

Pseudomonas aeruginosa

UniProt Q932P5

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 20–239 Not recorded ZN ZINC ION × 2 ACY ACETIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;293 K;drop contained 5 uL protein (14mg/mL in 20mM HEPES, pH 7.5) with 5 uL reservoir (0.2M sodium acetate, 30% PEG4000, 0.1M sodium citrate pH 5.6). Crystal grew as plates after 2 weeks., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 3.10 Å R-free 0.288

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name Q932P5_9GAMM
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–220; UniProt 20–239

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 1ddk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ddk
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id1ddk
Deposition date deposition_date1999-11-10
Structure title titleCRYSTAL STRUCTURE OF IMP-1 METALLO BETA-LACTAMASE FROM PSEUDOMONAS AERUGINOSA
Keywords keywordsIMP-1 METALLO BETA-LACTAMASE, BINUCLEAR METAL CENTER, ZN BETA-LACTAMASE, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier17.67
Radius of gyration Rg (electron density) rg_electron16.53
Forward intensity I(0) i010053200.00
Molecular weight molecular_weight24494.0 kDa
Excluded volume excluded_volume31090 ų
Envelope volume envelope_volume34811 ų
Hydration-shell volume shell_volume17335 ų
Envelope diameter envelope_diameter59.0
Shell Rg shell_rg23.08
Envelope Rg envelope_rg16.91
Shape Rg shape_rg16.51
Total Rg total_rg17.69
Total atoms total_atoms1728
Residues n_residues220
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 dmax57.9
Rg (real space) rg_real17.56
Rg uncertainty (real space) rg_real_error0.39
I(0) (real space) i0_real1.0050e+07
I(0) uncertainty (real space) i0_real_error1.2840e+05
Rg (reciprocal space) rg_reciprocal17.57
I(0) (reciprocal space) i0_reciprocal10050000.0000
Solution quality estimate total_estimate0.7938
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary23.1
Skewness Skewness skewness0.193
Kurtosis Kurtosis kurtosis-0.269
Angular range angular_range— – 0.4500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2894000.0000
Real-space data points n_real_points76
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.775; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1ddka_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.157 — Metallo-hydrolase/oxidoreductase
Superfamily Superfamily superfamilyd.157.1 — Metallo-hydrolase/oxidoreductase
Family Family familyd.157.1.1 — Zn metallo-beta-lactamase

CATH v4.4 (1 domains)

Domain ID domain_id1ddkA00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology15 — Metallo-beta-lactamase; Chain A
Homologous superfamily homologous superfamily10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

8. Citations (1)

9. Files and Curves (10)