1cp9

CRYSTAL STRUCTURE OF PENICILLIN G ACYLASE FROM THE BRO1 MUTANT STRAIN OF PROVIDENCIA RETTGERI

Method: X-RAY DIFFRACTION Dmax: 88.6 Å Quality: GOOD

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

Penicillin G amidase

OrganismNot specified

UniProt Q7WZI9

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 24–228 Chain B; UniProt 285–837 Fragment:UNP residues 24-228 Mutation:M140L Non-standard monomer:Yes (specific site not provided by mmCIF) Fragment:UNP residues 285-837 SO4 SULFATE ION × 4 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.5;PROTEIN WAS CRYSTALLIZED FROM 30-45% SATURATED AMMONIUM SULFATE, 15% GLYCEROL, 50 MM K2HPO4, 0.02% W/V SODIUM AZIDE, PH 7.5 Resolution 2.50 Å R-free 0.165
2 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 24–228 Chain B; UniProt 285–837 Fragment:UNP residues 24-228 Mutation:M140L Non-standard monomer:Yes (specific site not provided by mmCIF) Fragment:UNP residues 285-837 SO4 SULFATE ION × 8 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.5;PROTEIN WAS CRYSTALLIZED FROM 30-45% SATURATED AMMONIUM SULFATE, 15% GLYCEROL, 50 MM K2HPO4, 0.02% W/V SODIUM AZIDE, PH 7.5 Resolution 2.50 Å R-free 0.165

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 Q7WZI9_PRORE
Isoform
PDB entities 1, 2
Chains and sequence ranges Author chain A; PDBConstruct 1–205; UniProt 24–228 Author chain B; PDBConstruct 1–553; UniProt 285–837

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 1cp9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1cp9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1cp9
Deposition date deposition_date1999-06-12
Structure title titleCRYSTAL STRUCTURE OF PENICILLIN G ACYLASE FROM THE BRO1 MUTANT STRAIN OF PROVIDENCIA RETTGERI
Keywords keywords;ANTIBIOTIC RESISTANCE, AMIDOHYDROLASE, NTN-HYDROLASE FOLD, N-TERMINAL PYROGLUTAMATE, PENICILLIN BINDING PROTEIN, CALCIUM BINDING PROTEIN, HYDROLASE ;; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier27.71
Radius of gyration Rg (electron density) rg_electron26.52
Forward intensity I(0) i0118571000.00
Molecular weight molecular_weight85352.0 kDa
Excluded volume excluded_volume106200 ų
Envelope volume envelope_volume122760 ų
Hydration-shell volume shell_volume37196 ų
Envelope diameter envelope_diameter94.7
Shell Rg shell_rg35.20
Envelope Rg envelope_rg26.68
Shape Rg shape_rg26.47
Total Rg total_rg27.46
Total atoms total_atoms6038
Residues n_residues749
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 dmax88.6
Rg (real space) rg_real27.54
Rg uncertainty (real space) rg_real_error0.42
I(0) (real space) i0_real1.1860e+08
I(0) uncertainty (real space) i0_real_error1.6090e+06
Rg (reciprocal space) rg_reciprocal27.59
I(0) (reciprocal space) i0_reciprocal118600000.0000
Solution quality estimate total_estimate0.8975
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.7
Skewness Skewness skewness0.167
Kurtosis Kurtosis kurtosis-0.460
Angular range angular_range— – 0.2850 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha26760000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.892; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.994

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1cp9.1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.153 — Ntn hydrolase-like
Superfamily Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family familyd.153.1.2 — Penicillin acylase, catalytic domain

CATH v4.4 (5 domains)

Domain ID domain_id1cp9A01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology439 — Penicillin Amidohydrolase; domain 1
Homologous superfamily homologous superfamily10 — Penicillin Amidohydrolase, domain 1
Domain ID domain_id1cp9A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily150
Domain ID domain_id1cp9B01
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
Domain ID domain_id1cp9B02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology120 — Penicillin G acylase, beta-roll domain
Homologous superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region
Domain ID domain_id1cp9B03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1400 — Penicillin amidase (Acylase) alpha subunit, N-terminal domain
Homologous superfamily homologous superfamily10 — Aminohydrolase, alpha-helical knob region

8. Citations (1)

9. Files and Curves (10)