4E55 | pdb_00004e55

Crystal Structure of spacer removed cephalosporin acylase mutant

• PDB DOI: https://doi.org/10.2210/pdb4E55/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Spacer shortened Cephalosporin acylase

Yin, J., Zhang, Z., Wu, G., Huang, X.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 154.75 kDa 
• Atom Count: 11,411 
• Modeled Residue Count: 1,330 
• Deposited Residue Count: 1,388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cephalosporin acylase	A, B	694	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.238	α = 90
b = 74.238	β = 90
c = 383.86	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

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

Revision History  

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