1amp

CRYSTAL STRUCTURE OF AEROMONAS PROTEOLYTICA AMINOPEPTIDASE: A PROTOTYPICAL MEMBER OF THE CO-CATALYTIC ZINC ENZYME FAMILY

Method: X-RAY DIFFRACTION Dmax: 56.2 Å Quality: GOOD

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

AMINOPEPTIDASE

Vibrio proteolyticus

UniProt Q01693

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 107–397 Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.80 Å

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.

21 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AMPX_VIBPR
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–291; UniProt 107–397

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 1amp

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1amp
Deposition date deposition_date1994-04-22
Structure title titleCRYSTAL STRUCTURE OF AEROMONAS PROTEOLYTICA AMINOPEPTIDASE: A PROTOTYPICAL MEMBER OF THE CO-CATALYTIC ZINC ENZYME FAMILY
Keywords keywordsHYDROLASE(AMINOPEPTIDASE); HYDROLASE(AMINOPEPTIDASE)
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier18.41
Radius of gyration Rg (electron density) rg_electron17.26
Forward intensity I(0) i018488200.00
Molecular weight molecular_weight31503.0 kDa
Excluded volume excluded_volume38727 ų
Envelope volume envelope_volume41922 ų
Hydration-shell volume shell_volume19698 ų
Envelope diameter envelope_diameter58.0
Shell Rg shell_rg24.12
Envelope Rg envelope_rg17.45
Shape Rg shape_rg17.27
Total Rg total_rg18.11
Total atoms total_atoms2212
Residues n_residues291
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 dmax56.2
Rg (real space) rg_real18.27
Rg uncertainty (real space) rg_real_error0.23
I(0) (real space) i0_real1.8490e+07
I(0) uncertainty (real space) i0_real_error1.9040e+05
Rg (reciprocal space) rg_reciprocal18.29
I(0) (reciprocal space) i0_reciprocal18490000.0000
Solution quality estimate total_estimate0.8211
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.9
Skewness Skewness skewness0.067
Kurtosis Kurtosis kurtosis-0.453
Angular range angular_range— – 0.4300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5323000.0000
Real-space data points n_real_points74
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.899; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1ampa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamilyc.56.5 — Zn-dependent exopeptidases
Family Family familyc.56.5.4 — Bacterial dinuclear zinc exopeptidases

CATH v4.4 (1 domains)

Domain ID domain_id1ampA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases

8. Citations (2)

9. Files and Curves (10)