3FMC | pdb_00003fmc

CRYSTAL STRUCTURE OF a putative succinylglutamate desuccinylase / aspartoacylase family protein (SAMA_0604) FROM SHEWANELLA AMAZONENSIS SB2B AT 1.80 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb3FMC/pdb

• Classification: HYDROLASE
• Organism(s): Shewanella amazonensis SB2B
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-12-19 Released: 2009-01-06 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Literature

Crystal structure of putative succinylglutamate desuccinylase / aspartoacylase (YP_926482.1) from Shewanella amazonensis SB2B at 1.80 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)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 166.66 kDa 
• Atom Count: 13,752 
• Modeled Residue Count: 1,461 
• Deposited Residue Count: 1,472 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative succinylglutamate desuccinylase / aspartoacylase	A, B, C, D	368	Shewanella amazonensis SB2B	Mutation(s): 0  Gene Names: Sama_0604, YP_926482.1
UniProt
Find proteins for A1S356 (Shewanella amazonensis (strain ATCC BAA-1098 / SB2B)) Explore A1S356  Go to UniProtKB:  A1S356

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], G [auth B], K [auth C], M [auth D], N [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], H [auth B], I [auth B], J [auth B], L [auth C], O [auth D], P [auth D], Q [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33FMC

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.279	α = 90
b = 140.101	β = 90
c = 164.17	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-06 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-01-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary