5THK | pdb_00005thk

Crystal Structure of a Putative Dehydrogenase from Burkholderia cenocepacia with bound NADP

PDB DOI: https://doi.org/10.2210/pdb5THK/pdb

Classification: OXIDOREDUCTASE
Organism(s): Burkholderia cenocepacia J2315
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-09-29 Released: 2016-10-12
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.164 (Depositor), 0.164 (DCC)
R-Value Work:
0.140 (Depositor), 0.139 (DCC)
R-Value Observed:
0.140 (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 a Putative Dehydrogenase from Burkholderia cenocepacia with bound NADP

Dranow, D.M., Mayclin, S.J., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 232.9 kDa
Atom Count: 18,993
Modeled Residue Count: 2,056
Deposited Residue Count: 2,128
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	266	Burkholderia cenocepacia J2315	Mutation(s): 0 Gene Names: BCAL2694
UniProt
Find proteins for B4E8W7 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4E8W7 Go to UniProtKB: B4E8W7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B4E8W7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] SDF format, chain P [auth F] SDF format, chain Q [auth G] SDF format, chain S [auth H] SDF format, chain O [auth E] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] MOL2 format, chain P [auth F] MOL2 format, chain Q [auth G] MOL2 format, chain S [auth H] MOL2 format, chain O [auth E] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D] mmCIF format, chain P [auth F] mmCIF format, chain Q [auth G] mmCIF format, chain S [auth H] mmCIF format, chain O [auth E]	I [auth A] J [auth B] K [auth C] N [auth D] O [auth E] I [auth A], J [auth B], K [auth C], N [auth D], O [auth E], P [auth F], Q [auth G], S [auth H]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain S [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain S [auth H]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain T [auth H] MOL2 format, chain M [auth C] MOL2 format, chain T [auth H] mmCIF format, chain M [auth C] mmCIF format, chain T [auth H]	M [auth C], T [auth H]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Focus chain T [auth H] Interactions & Density Focus chain M [auth C] Focus chain T [auth H]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain R [auth G] MOL2 format, chain L [auth C] MOL2 format, chain R [auth G] mmCIF format, chain L [auth C] mmCIF format, chain R [auth G]	L [auth C], R [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain L [auth C] Focus chain R [auth G] Interactions & Density Focus chain L [auth C] Focus chain R [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.164 (Depositor), 0.164 (DCC)
R-Value Work: 0.140 (Depositor), 0.139 (DCC)
R-Value Observed: 0.140 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.54	α = 90
b = 102.44	β = 97.28
c = 122.25	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-10-12

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2016-10-12
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description

5THK | pdb_00005thk

Crystal Structure of a Putative Dehydrogenase from Burkholderia cenocepacia with bound NADP

Literature

Crystal Structure of a Putative Dehydrogenase from Burkholderia cenocepacia with bound NADP

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Biological Assembly 5

Biological Assembly 6

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)