2QUY | pdb_00002quy

Truncated mutant ASN175ALA of penicillin v acylase from bacillus sphaericus

PDB DOI: https://doi.org/10.2210/pdb2QUY/pdb

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

Deposited: 2007-08-07 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: 1.70 Å
R-Value Free:
0.203 (Depositor), 0.204 (DCC)
R-Value Work:
0.175 (Depositor), 0.178 (DCC)
R-Value Observed:
0.177 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Auto-proteolytic processing of Penicillin V Acylase is simpler than of other related Ntn hydrolases

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

To be published.

Macromolecule Content

Total Structure Weight: 297.9 kDa
Atom Count: 21,995
Modeled Residue Count: 2,637
Deposited Residue Count: 2,680
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin acylase	A, B, C, D, E A, B, C, D, E, F, G, H	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
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain P [auth H] SDF format, chain O [auth G] SDF format, chain N [auth E] SDF format, chain M [auth E] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain J [auth B] SDF format, chain I [auth A] MOL2 format, chain P [auth H] MOL2 format, chain O [auth G] MOL2 format, chain N [auth E] MOL2 format, chain M [auth E] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] mmCIF format, chain P [auth H] mmCIF format, chain O [auth G] mmCIF format, chain N [auth E] mmCIF format, chain M [auth E] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A]	I [auth A] J [auth B] K [auth C] L [auth C] M [auth E] I [auth A], J [auth B], K [auth C], L [auth C], M [auth E], N [auth E], O [auth G], P [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth E] Focus chain N [auth E] Focus chain O [auth G] Focus chain P [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth E] Focus chain N [auth E] Focus chain O [auth G] Focus chain P [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.203 (Depositor), 0.204 (DCC)
R-Value Work: 0.175 (Depositor), 0.178 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.286	α = 90
b = 379.383	β = 93.51
c = 102.013	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: 2024-05-29
Changes: Data collection

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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.