4E56 | pdb_00004e56

Crystal Structure of spacer 8aa-shortened cephalosporin acylase mutant

PDB DOI: https://doi.org/10.2210/pdb4E56/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas sp. 130
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-03-14 Released: 2013-03-20
Deposition Author(s): Yin, J., Zhang, Z., Wu, G., Huang, X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.202 (Depositor), 0.199 (DCC)
R-Value Work:
0.173 (Depositor), 0.171 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4E56

This is version 1.1 of the entry. See complete history.

Literature

spacer shortened Cephalosporin acylase

Yin, J., Zhang, Z., Wu, G., Huang, X.

To be published.

Macromolecule Content

Total Structure Weight: 154.97 kDa
Atom Count: 11,706
Modeled Residue Count: 1,328
Deposited Residue Count: 1,392
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cephalosporin acylase	A, B	696	Pseudomonas sp. 130	Mutation(s): 1 Gene Names: CA, ca1 EC: 3.5.1.93
UniProt
Find proteins for O86089 (Pseudomonas sp. 130) Explore O86089 Go to UniProtKB: O86089
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O86089
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.202 (Depositor), 0.199 (DCC)
R-Value Work: 0.173 (Depositor), 0.171 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.743	α = 90
b = 73.743	β = 90
c = 383.726	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-03-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-03-20
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, 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.