5WOL | pdb_00005wol

Crystal structure of dihydrodipicolinate reductase DapB from Coxiella burnetii

PDB DOI: https://doi.org/10.2210/pdb5WOL/pdb

Classification: OXIDOREDUCTASE
Organism(s): Coxiella burnetii RSA 493
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-08-02 Released: 2017-08-16
Deposition Author(s): Stogios, P.J., Wawrzak, Z., Onopriyenko, O., Grimshaw, S., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.218 (Depositor), 0.219 (DCC)
R-Value Work:
0.178 (Depositor), 0.178 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of dihydrodipicolinate reductase DapB from Coxiella burnetii

Stogios, P.J.

To be published.

Macromolecule Content

Total Structure Weight: 28.08 kDa
Atom Count: 2,117
Modeled Residue Count: 230
Deposited Residue Count: 239
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-tetrahydrodipicolinate reductase	A	239	Coxiella burnetii RSA 493	Mutation(s): 0 Gene Names: dapB, CBU_1709 EC: 1.17.1.8
UniProt
Find proteins for P24703 (Coxiella burnetii (strain RSA 493 / Nine Mile phase I)) Explore P24703 Go to UniProtKB: P24703
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P24703
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PE3 Query on PE3 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL C₂₈ H₅₈ O₁₅ ILLKMACMBHTSHP-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
6PC Query on 6PC Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A]	PYRIDINE-2-CARBOXYLIC ACID C₆ H₅ N O₂ SIOXPEMLGUPBBT-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.218 (Depositor), 0.219 (DCC)
R-Value Work: 0.178 (Depositor), 0.178 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.605	α = 90
b = 78.795	β = 90
c = 84.074	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-08-16

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C

Revision History (Full details and data files)

Version 1.0: 2017-08-16
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence
Version 1.2: 2019-12-11
Changes: Author supporting evidence
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description