4CKZ | pdb_00004ckz

Structure of the Mycobacterium tuberculosis Type II Dehydroquinase D88N mutant

• PDB DOI: https://doi.org/10.2210/pdb4CKZ/pdb

• Classification: LYASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2014-01-10 Released: 2015-03-25 
• Deposition Author(s): Otero, J.M., Llamas-Saiz, A.L., Maneiro, M., Peon, A., Sedes, A., Lamb, H., Hawkins, A.R., Gonzalez-Bello, C., van Raaij, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 
  0.336 (Depositor), 0.350 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Starting Model: experimental

Literature

Investigation of the Dehydratation Mechanism Catalyzed by the Type II Dehydroquinase

Maneiro, M., Otero, J.M., Peon, A., Sedes, A., Llamas-Saiz, A.L., Lamb, H., Hawkins, A.R., van Raaij, M.J., Gonzalez-Bello, C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 31.35 kDa 
• Atom Count: 1,938 
• Modelled Residue Count: 256 
• Deposited Residue Count: 292 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-DEHYDROQUINATE DEHYDRATASE	A, B	146	Mycobacterium tuberculosis	Mutation(s): 1  EC: 4.2.1.10
UniProt
Find proteins for P9WPX7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPX7  Go to UniProtKB:  P9WPX7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free:  0.336 (Depositor), 0.350 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.42	α = 90
b = 38.42	β = 90
c = 132	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-25 
Deposition Author(s): Otero, J.M., Llamas-Saiz, A.L., Maneiro, M., Peon, A., Sedes, A., Lamb, H., Hawkins, A.R., Gonzalez-Bello, C., van Raaij, M.J.

Revision History  

• Version 1.0: 2015-03-25
  Type: Initial release
  
• Version 1.1: 2016-06-15
  Changes: Database references, Structure summary
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Other, Refinement description