3LWU | pdb_00003lwu

Crystal structure of Putative succinylglutamate desuccinylase/aspartoacylase (YP_749235.1) from Shewanella frigidimarinA NCIMB 400 at 2.10 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3LWU/pdb

• Classification: HYDROLASE
• Organism(s): Shewanella frigidimarina NCIMB 400
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-02-24 Released: 2010-03-23 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.190 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Literature

Crystal structure of Putative succinylglutamate desuccinylase/aspartoacylase (YP_749235.1) from Shewanella frigidimarina NCIMB 400 at 2.10 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 44.04 kDa 
• Atom Count: 3,136 
• Modeled Residue Count: 372 
• Deposited Residue Count: 391 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinylglutamate desuccinylase/aspartoacylase	A	391	Shewanella frigidimarina NCIMB 400	Mutation(s): 0  Gene Names: Sfri_0536
UniProt
Find proteins for Q088B8 (Shewanella frigidimarina (strain NCIMB 400)) Explore Q088B8  Go to UniProtKB:  Q088B8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
UNL	B [auth A]	Unknown ligand PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.190 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33LWU

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.549	α = 90
b = 128.972	β = 90
c = 129.574	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-23 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-03-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary