6M5N | pdb_00006m5n

Apo-Form Structure of Borneol Dehydrogenase

• PDB DOI: https://doi.org/10.2210/pdb6M5N/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas sp. TCU-HL1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-03-11 Released: 2020-07-15 
• Deposition Author(s): Khine, A.A., Huang, K.F., Ko, T.P., Chen, H.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 
  0.181 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Structural characterization of borneol dehydrogenase from Pseudomonas sp. TCU-HL1

Khine, A.A., Huang, K.F., Ko, T.P., Chen, H.P.

(2020) Acta Crystallogr F Struct Biol Commun 76: 309-313

• DOI: https://doi.org/10.1107/S2053230X20008584

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 (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 27.91 kDa 
• Atom Count: 2,229 
• Modeled Residue Count: 259 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Borneol dehydrogenase	A	260	Pseudomonas sp. TCU-HL1	Mutation(s): 0  Gene Names: THL1_4180

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	C [auth A], D [auth A], E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.181 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.629	α = 90
b = 96.507	β = 90
c = 142.562	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-15 
Deposition Author(s): Khine, A.A., Huang, K.F., Ko, T.P., Chen, H.P.

Revision History  

• Version 1.0: 2020-07-15
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description