2Z71 | pdb_00002z71

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 (Depositor)
R-Value Work:
0.239 (Depositor)
R-Value Observed:
0.240 (Depositor)

Starting Model: experimental
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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
Modeled Residue Count: 661
Deposited Residue Count: 670
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF format, chain C [auth A] mmCIF 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 (Depositor)
R-Value Work: 0.239 (Depositor)
R-Value Observed: 0.240 (Depositor)

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

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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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.