1GQO | pdb_00001gqo

Type II Dehydroquinase from Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb1GQO/pdb

• Classification: LYASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2001-11-28 Released: 2002-12-12 
• Deposition Author(s): Robinson, D.A., Roszak, A.W., Coggins, J.R., Lapthorn, A.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.259 (Depositor) 
• R-Value Work: 
  0.201 (Depositor) 

Starting Model: other

Literature

Crystal Structure of the Type II Dehydroquinase from Bacillus Subtilis

Robinson, D.A., Roszak, A.W., Coggins, J.R., Lapthorn, A.J.

To be published.

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

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

Biological Assembly 2  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 387.91 kDa 
• Atom Count: 28,764 
• Modeled Residue Count: 3,381 
• Deposited Residue Count: 3,432 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DEHYDROQUINASE	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W [auth X], X [auth Y]	143	Bacillus subtilis	Mutation(s): 0  Gene Names: YQHS EC: 4.2.1.10
UniProt
Find proteins for P54517 (Bacillus subtilis (strain 168)) Explore P54517  Go to UniProtKB:  P54517

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	AA [auth A], AB [auth J], AC [auth S], BA [auth B], BB [auth J], BC [auth S], CA [auth B], CB [auth K], CC [auth S], DA [auth B], DB [auth K], DC [auth T], EA [auth C], EB [auth K], EC [auth T], FA [auth C], FB [auth L], FC [auth T], GA [auth C], GB [auth L], GC [auth U], HA [auth D], HB [auth L], HC [auth U], IA [auth D], IB [auth M], IC [auth U], JA [auth D], JB [auth M], JC [auth V], KA [auth E], KB [auth M], KC [auth V], LA [auth E], LB [auth N], LC [auth V], MA [auth E], MB [auth N], MC [auth X], NA [auth F], NB [auth N], NC [auth X], OA [auth F], OB [auth O], OC [auth X], PA [auth F], PB [auth O], PC [auth Y], QA [auth G], QB [auth O], QC [auth Y], RA [auth G], RB [auth P], RC [auth Y], SA [auth G], SB [auth P], TA [auth H], TB [auth P], UA [auth H], UB [auth Q], VA [auth H], VB [auth Q], WA [auth I], WB [auth Q], XA [auth I], XB [auth R], Y [auth A], YA [auth I], YB [auth R], Z [auth A], ZA [auth J], ZB [auth R]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.259 (Depositor) 
• R-Value Work:  0.201 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.21	α = 90
b = 195.61	β = 91.87
c = 97.36	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-12-12 
Deposition Author(s): Robinson, D.A., Roszak, A.W., Coggins, J.R., Lapthorn, A.J.

Revision History  

• Version 1.0: 2002-12-12
  Type: Initial release
  
• Version 1.1: 2011-09-07
  Changes: Atomic model, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Refinement description