3QQW | pdb_00003qqw

Crystal structure of a putative lyase (Reut_B4148) from Ralstonia eutropha JMP134 at 2.44 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3QQW/pdb

• Classification: LYASE
• Organism(s): Cupriavidus pinatubonensis JMP134
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-02-16 Released: 2011-03-02 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 
  0.231 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

Crystal structure of a Hypothetical lyase (Reut_B4148) from Ralstonia eutropha JMP134 at 2.44 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 219.58 kDa 
• Atom Count: 13,240 
• Modeled Residue Count: 1,739 
• Deposited Residue Count: 1,992 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative citrate lyase	A, B, C, D, E, F	332	Cupriavidus pinatubonensis JMP134	Mutation(s): 0  Gene Names: Reut_B4148
UniProt
Find proteins for Q46TN2 (Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197)) Explore Q46TN2  Go to UniProtKB:  Q46TN2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	G [auth A], H [auth B], I [auth B], J [auth C], K [auth C], L [auth D], M [auth E], N [auth E], O [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free:  0.231 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33QQW

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 226.401	α = 90
b = 73.826	β = 125.31
c = 149.252	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-02 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2011-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-07-20
  Changes: Structure summary
• Version 1.3: 2014-12-24
  Changes: Structure summary
• Version 1.4: 2017-11-08
  Changes: Refinement description
• Version 1.5: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary