2PGO | pdb_00002pgo

The crystal structure of FAD and ThDP dependent Cyclohexane-1,2-dione Hydrolase (Cdh) from Azoarcus sp. strain 22Lin

• PDB DOI: https://doi.org/10.2210/pdb2PGO/pdb

• Classification: HYDROLASE
• Organism(s): Azoarcus sp.
• Mutation(s): No 


• Deposited: 2007-04-10 Released: 2008-04-22 
• Deposition Author(s): Steinbach, A.K., Warkentin, E., Kroneck, P.M.H., Ermler, U.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free: 
  0.120 (Depositor), 0.144 (DCC) 
• R-Value Work: 
  0.097 (Depositor) 
• R-Value Observed: 
  0.098 (Depositor) 

Literature

The crystal structure of FAD and ThDP dependent Cyclohexane-1,2-dione Hydrolase (Cdh) from Azoarcus sp. strain 22Lin

Steinbach, A.K., Harder, J., Warkentin, E., Kroneck, P.M.H., Ermler, U.

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 129.6 kDa 
• Atom Count: 10,640 
• Modeled Residue Count: 1,174 
• Deposited Residue Count: 1,178 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclohexane-1,2-dione Hydrolase (Cdh)	A, B	589	Azoarcus sp.	Mutation(s): 0  EC: 3.7.1.11
UniProt
Find proteins for P0CH62 (Azoarcus sp) Explore P0CH62  Go to UniProtKB:  P0CH62

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	E [auth A], L [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
TPP	F [auth A], M [auth B]	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O
MPD	G [auth A], H [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4	I [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	D [auth A], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free:  0.120 (Depositor), 0.144 (DCC) 
• R-Value Work:  0.097 (Depositor) 
• R-Value Observed: 0.098 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.6	α = 90
b = 123.6	β = 90
c = 144.3	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-22 
Deposition Author(s): Steinbach, A.K., Warkentin, E., Kroneck, P.M.H., Ermler, U.

Revision History  

• Version 1.0: 2008-04-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations