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), 0.251 (DCC)
R-Value Work:
0.196 (Depositor), 0.196 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

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

Cheng, W.C., Chen, T.J., Wang, W.C.

To be published.

Macromolecule Content

Total Structure Weight: 79.31 kDa
Atom Count: 5,260
Modeled Residue Count: 686
Deposited Residue Count: 736
Unique protein chains: 1

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WPX9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.47 Å
R-Value Free: 0.258 (Depositor), 0.251 (DCC)
R-Value Work: 0.196 (Depositor), 0.196 (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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-01-18

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.