3VWO | pdb_00003vwo

Crystal structure of peptidoglycan hydrolase mutant from Sphingomonas sp. A1

• PDB DOI: https://doi.org/10.2210/pdb3VWO/pdb

• Classification: HYDROLASE
• Organism(s): Sphingomonas sp. A1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-08-30 Released: 2013-09-04 
• Deposition Author(s): Maruyama, Y., Mikami, B., Hashimoto, W., Murata, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.234 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of peptidoglycan hydrolase mutant from Sphingomonas sp. A1

Maruyama, Y., Mikami, B., Hashimoto, W., Murata, K.

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)

Macromolecule Content 

• Total Structure Weight: 18.2 kDa 
• Atom Count: 1,286 
• Modeled Residue Count: 155 
• Deposited Residue Count: 161 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan hydrolase FlgJ	A	161	Sphingomonas sp. A1	Mutation(s): 0  Gene Names: flgJ
UniProt
Find proteins for B7XH69 (Sphingomonas sp. A1) Explore B7XH69  Go to UniProtKB:  B7XH69

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	B [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.234 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.467	α = 90
b = 48.467	β = 90
c = 124.203	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-04 
Deposition Author(s): Maruyama, Y., Mikami, B., Hashimoto, W., Murata, K.

Revision History  

• Version 1.0: 2013-09-04
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description