3HDU

CRYSTAL STRUCTURE OF A PUTATIVE THIOESTERASE (SYN_01977) FROM SYNTROPHUS ACIDITROPHICUS SB AT 2.50 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb3HDU/pdb

• Classification: HYDROLASE
• Organism(s): Syntrophus aciditrophicus SB
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-07 Released: 2009-06-02 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.257 
• R-Value Work: 0.237 
• R-Value Observed: 0.238 

Literature

Crystal structure of putative thioesterase (YP_461911.1) from SYNTROPHUS ACIDITROPHICUS SB at 2.50 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 54.06 kDa 
• Atom Count: 3,438 
• Modelled Residue Count: 451 
• Deposited Residue Count: 471 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative thioesterase	A, B, C	157	Syntrophus aciditrophicus SB	Mutation(s): 0  Gene Names: SYNAS_18640, SYN_01977, YP_461911.1
UniProt
Find proteins for Q2LUI2 (Syntrophus aciditrophicus (strain SB)) Explore Q2LUI2  Go to UniProtKB:  Q2LUI2

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.257 
• R-Value Work: 0.237 
• R-Value Observed: 0.238 
• Space Group: P 4₃ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/M33HDU

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.165	α = 90
b = 117.165	β = 90
c = 71.602	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-02 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references