3C6C | pdb_00003c6c

Crystal structure of a putative 3-keto-5-aminohexanoate cleavage enzyme (reut_c6226) from ralstonia eutropha jmp134 at 1.72 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3C6C/pdb

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


• Deposited: 2008-02-04 Released: 2008-02-19 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 
  0.184 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Literature

Crystal structure of 3-keto-5-aminohexanoate cleavage enzyme (YP_293392.1) from Ralstonia eutropha JMP134 at 1.72 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 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.26 kDa 
• Atom Count: 2,667 
• Modelled Residue Count: 294 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-keto-5-aminohexanoate cleavage enzyme	A	316	Cupriavidus pinatubonensis JMP134	Mutation(s): 0  Gene Names: YP_293392.1, Reut_C6226
UniProt
Find proteins for Q46MU0 (Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197)) Explore Q46MU0  Go to UniProtKB:  Q46MU0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	G [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NI	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-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: 1.72 Å
• R-Value Free:  0.184 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33C6C

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.339	α = 90
b = 121.397	β = 90
c = 133.028	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-19 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-02-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  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
• Version 1.5: 2024-11-20
  Changes: Data collection, Structure summary