2Z71

Structure of truncated mutant CYS1GLY of penicillin V acylase from bacillus sphaericus co-crystallized with penicillin V

PDB DOI: https://doi.org/10.2210/pdb2Z71/pdb

Classification: HYDROLASE
Organism(s): Lysinibacillus sphaericus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-08-10 Released: 2008-08-26
Deposition Author(s): Pathak, M.C., Brannigan, J., Dodson, G.G., Suresh, C.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.270
R-Value Work: 0.239
R-Value Observed: 0.240

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Studies on the catalysis and post translational processing of penicillin V acylase

Pathak, M.C., Brannigan, J., Dodson, G.G., Suresh, C.G.

To be published.

Macromolecule Content

Total Structure Weight: 75.1 kDa
Atom Count: 5,260
Modelled Residue Count: 661
Deposited Residue Count: 670
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin acylase	A, B [auth C]	335	N/A	Mutation(s): 1 EC: 3.5.1.11
UniProt
Find proteins for P12256 (Lysinibacillus sphaericus) Explore P12256 Go to UniProtKB: P12256
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12256
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PNV Query on PNV Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth C] MOL2 format, chain C [auth A] MOL2 format, chain D [auth C]	C [auth A], D [auth C]	(2S,5R,6R)-3,3-DIMETHYL-7-OXO-6-(2-PHENOXYACETAMIDO)-4-THIA-1- AZABICYCLO(3.2.0)HEPTANE-2-CARBOXYLIC ACID C₁₆ H₁₈ N₂ O₅ S BPLBGHOLXOTWMN-MBNYWOFBSA-N		Interactions Focus chain C [auth A] Focus chain D [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.270
R-Value Work: 0.239
R-Value Observed: 0.240
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.73	α = 90
b = 158.89	β = 90
c = 90.742	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-08-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-08-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-11-10
Changes: Database references, Derived calculations
Version 1.3: 2023-11-01
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.