3IUZ | pdb_00003iuz

Crystal structure of Putative glyoxalase superfamily protein (YP_299723.1) from RALSTONIA EUTROPHA JMP134 at 1.90 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3IUZ/pdb

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


• Deposited: 2009-08-31 Released: 2009-09-08 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.206 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.167 (Depositor) 
• R-Value Observed: 
  0.169 (Depositor) 

Literature

Crystal structure of Putative glyoxalase superfamily protein (YP_299723.1) from RALSTONIA EUTROPHA JMP134 at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

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: 38.52 kDa 
• Atom Count: 2,884 
• Modeled Residue Count: 320 
• Deposited Residue Count: 340 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative glyoxalase superfamily protein	A	340	Cupriavidus pinatubonensis JMP134	Mutation(s): 0  Gene Names: Reut_B5534, YP_299723.1 EC: 1.13.11.93
UniProt
Find proteins for Q46PQ5 (Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197)) Explore Q46PQ5  Go to UniProtKB:  Q46PQ5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6G	B [auth A]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
PGE	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	A	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.206 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.167 (Depositor) 
• R-Value Observed: 0.169 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33IUZ

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.069	α = 90
b = 114.069	β = 90
c = 133.518	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: 2009-09-08 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, 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, Derived calculations