4XGN | pdb_00004xgn

Crystal structure of 3-hydroxyacyl-CoA dehydrogenase in complex with NAD from Burkholderia thailandensis

PDB DOI: https://doi.org/10.2210/pdb4XGN/pdb

Classification: OXIDOREDUCTASE
Organism(s): Burkholderia thailandensis E264
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-12-31 Released: 2015-01-14
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.177 (Depositor), 0.190 (DCC)
R-Value Work:
0.154 (Depositor), 0.170 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of 3-hydroxyacyl-CoA dehydrogenase in complex with NAD from Burkholderia thailandensis

Abendroth, J., Dranow, D.M., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 223.07 kDa
Atom Count: 17,056
Modeled Residue Count: 2,037
Deposited Residue Count: 2,080
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-hydroxyacyl-CoA dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	260	Burkholderia thailandensis E264	Mutation(s): 0 Gene Names: BTH_I0738
UniProt
Find proteins for Q2T0K5 (Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CCUG 48851 / CIP 106301 / E264)) Explore Q2T0K5 Go to UniProtKB: Q2T0K5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2T0K5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain Y [auth F] SDF format, chain V [auth E] SDF format, chain S [auth D] SDF format, chain O [auth C] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain GA [auth H] SDF format, chain CA [auth G] MOL2 format, chain Y [auth F] MOL2 format, chain V [auth E] MOL2 format, chain S [auth D] MOL2 format, chain O [auth C] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain GA [auth H] MOL2 format, chain CA [auth G] mmCIF format, chain Y [auth F] mmCIF format, chain V [auth E] mmCIF format, chain S [auth D] mmCIF format, chain O [auth C] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain GA [auth H] mmCIF format, chain CA [auth G]	CA [auth G] GA [auth H] I [auth A] L [auth B] O [auth C] CA [auth G], GA [auth H], I [auth A], L [auth B], O [auth C], S [auth D], V [auth E], Y [auth F]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain CA [auth G] Focus chain GA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Y [auth F] Interactions & Density Focus chain CA [auth G] Focus chain GA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Y [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain Q [auth C] SDF format, chain FA [auth H] SDF format, chain BA [auth G] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain FA [auth H] MOL2 format, chain BA [auth G] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain FA [auth H] mmCIF format, chain BA [auth G]	BA [auth G], FA [auth H], Q [auth C], R [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth G] Focus chain FA [auth H] Focus chain Q [auth C] Focus chain R [auth D] Interactions & Density Focus chain BA [auth G] Focus chain FA [auth H] Focus chain Q [auth C] Focus chain R [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain X [auth E] SDF format, chain W [auth E] SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain P [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain IA [auth H] SDF format, chain HA [auth H] SDF format, chain EA [auth G] SDF format, chain DA [auth G] SDF format, chain AA [auth F] MOL2 format, chain Z [auth F] MOL2 format, chain X [auth E] MOL2 format, chain W [auth E] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain P [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth H] MOL2 format, chain HA [auth H] MOL2 format, chain EA [auth G] MOL2 format, chain DA [auth G] MOL2 format, chain AA [auth F] mmCIF format, chain Z [auth F] mmCIF format, chain X [auth E] mmCIF format, chain W [auth E] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain P [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth H] mmCIF format, chain HA [auth H] mmCIF format, chain EA [auth G] mmCIF format, chain DA [auth G] mmCIF format, chain AA [auth F]	AA [auth F] DA [auth G] EA [auth G] HA [auth H] IA [auth H] AA [auth F], DA [auth G], EA [auth G], HA [auth H], IA [auth H], J [auth A], K [auth A], M [auth B], N [auth B], P [auth C], T [auth D], U [auth D], W [auth E], X [auth E], Z [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain IA [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain W [auth E] Focus chain X [auth E] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth F] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain IA [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain W [auth E] Focus chain X [auth E] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.177 (Depositor), 0.190 (DCC)
R-Value Work: 0.154 (Depositor), 0.170 (DCC)
R-Value Observed: 0.156 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34XGN

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.22	α = 103.26
b = 77.1	β = 93.98
c = 109.35	γ = 109.68

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
ARP	model building
Coot	model building
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-01-14

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2015-01-14
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary