3QBD | pdb_00003qbd

3-Dehydroquinate Synthase (aroB) from Mycobacterium tuberculosis in complex with NAD

• PDB DOI: https://doi.org/10.2210/pdb3QBD/pdb

• Classification: LYASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-01-13 Released: 2012-01-18 
• Deposition Author(s): Cheng, W.C., Chen, T.J., Wang, W.C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 
  0.258 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

3-Dehydroquinate Synthase (aroB) from Mycobacterium tuberculosis in complex with NAD

Cheng, W.C., Chen, T.J., Wang, W.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: 79.31 kDa 
• Atom Count: 5,260 
• Modelled Residue Count: 686 
• Deposited Residue Count: 736 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-dehydroquinate synthase	A, B	368	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: aroB, MRA_2566 EC: 4.2.3.4
UniProt
Find proteins for P9WPX9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPX9  Go to UniProtKB:  P9WPX9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], D [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free:  0.258 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.829	α = 90
b = 142.829	β = 90
c = 37.175	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-18 
Deposition Author(s): Cheng, W.C., Chen, T.J., Wang, W.C.

Revision History  

• Version 1.0: 2012-01-18
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description