7V0H | pdb_00007v0h

Crystal Structure of Putative glucose 1-dehydrogenase from Burkholderia cenocepacia in complex with NADP and a potential reaction product

PDB DOI: https://doi.org/10.2210/pdb7V0H/pdb

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

Deposited: 2022-05-10 Released: 2022-06-08
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.159 (Depositor), 0.159 (DCC)
R-Value Work:
0.139 (Depositor), 0.139 (DCC)
R-Value Observed:
0.139 (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 Putative glucose 1-dehydrogenase from Burkholderia cenocepacia in complex with NADP and a potential reaction product

Abendroth, J., DeBouwer, N.D., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 217.3 kDa
Atom Count: 17,404
Modeled Residue Count: 1,982
Deposited Residue Count: 2,048
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative glucose 1-dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	256	Burkholderia cenocepacia J2315	Mutation(s): 0 Gene Names: BCAL1425 EC: 1.1.1.47
UniProt
Find proteins for B4E6Z1 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4E6Z1 Go to UniProtKB: B4E6Z1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B4E6Z1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP (Subject of Investigation/LOI) Query on NAP Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain V [auth D] SDF format, chain T [auth C] SDF format, chain QA [auth H] SDF format, chain N [auth B] SDF format, chain MA [auth G] SDF format, chain I [auth A] SDF format, chain GA [auth F] MOL2 format, chain Z [auth E] MOL2 format, chain V [auth D] MOL2 format, chain T [auth C] MOL2 format, chain QA [auth H] MOL2 format, chain N [auth B] MOL2 format, chain MA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain GA [auth F] mmCIF format, chain Z [auth E] mmCIF format, chain V [auth D] mmCIF format, chain T [auth C] mmCIF format, chain QA [auth H] mmCIF format, chain N [auth B] mmCIF format, chain MA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain GA [auth F]	GA [auth F] I [auth A] MA [auth G] N [auth B] QA [auth H] GA [auth F], I [auth A], MA [auth G], N [auth B], QA [auth H], T [auth C], V [auth D], Z [auth E]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain GA [auth F] Focus chain I [auth A] Focus chain MA [auth G] Focus chain N [auth B] Focus chain QA [auth H] Focus chain T [auth C] Focus chain V [auth D] Focus chain Z [auth E] Interactions & Density Focus chain GA [auth F] Focus chain I [auth A] Focus chain MA [auth G] Focus chain N [auth B] Focus chain QA [auth H] Focus chain T [auth C] Focus chain V [auth D] Focus chain Z [auth E]
OUO (Subject of Investigation/LOI) Query on OUO Download:Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain JA [auth F] SDF format, chain L [auth A] SDF format, chain P [auth B] SDF format, chain PA [auth G] SDF format, chain RA [auth H] SDF format, chain U [auth C] SDF format, chain Y [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain JA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth G] MOL2 format, chain RA [auth H] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain DA [auth E] mmCIF format, chain JA [auth F] mmCIF format, chain L [auth A] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth G] mmCIF format, chain RA [auth H] mmCIF format, chain U [auth C] mmCIF format, chain Y [auth D]	DA [auth E] JA [auth F] L [auth A] P [auth B] PA [auth G] DA [auth E], JA [auth F], L [auth A], P [auth B], PA [auth G], RA [auth H], U [auth C], Y [auth D]	(2R)-2-(hydroxymethyl)pentanedioic acid C₆ H₁₀ O₅ XPQIPNORJZZYPV-SCSAIBSYSA-N		Interactions Focus chain DA [auth E] Focus chain JA [auth F] Focus chain L [auth A] Focus chain P [auth B] Focus chain PA [auth G] Focus chain RA [auth H] Focus chain U [auth C] Focus chain Y [auth D] Interactions & Density Focus chain DA [auth E] Focus chain JA [auth F] Focus chain L [auth A] Focus chain P [auth B] Focus chain PA [auth G] Focus chain RA [auth H] Focus chain U [auth C] Focus chain Y [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain NA [auth G] SDF format, chain J [auth A] SDF format, chain IA [auth F] SDF format, chain CA [auth E] SDF format, chain AA [auth E] MOL2 format, chain W [auth D] MOL2 format, chain NA [auth G] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain CA [auth E] MOL2 format, chain AA [auth E] mmCIF format, chain W [auth D] mmCIF format, chain NA [auth G] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth F] mmCIF format, chain CA [auth E] mmCIF format, chain AA [auth E]	AA [auth E] CA [auth E] IA [auth F] J [auth A] NA [auth G] AA [auth E], CA [auth E], IA [auth F], J [auth A], NA [auth G], W [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain CA [auth E] Focus chain IA [auth F] Focus chain J [auth A] Focus chain NA [auth G] Focus chain W [auth D] Interactions & Density Focus chain AA [auth E] Focus chain CA [auth E] Focus chain IA [auth F] Focus chain J [auth A] Focus chain NA [auth G] Focus chain W [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain S [auth B] SDF format, chain OA [auth G] SDF format, chain O [auth B] SDF format, chain K [auth A] SDF format, chain HA [auth F] SDF format, chain FA [auth E] SDF format, chain BA [auth E] MOL2 format, chain X [auth D] MOL2 format, chain S [auth B] MOL2 format, chain OA [auth G] MOL2 format, chain O [auth B] MOL2 format, chain K [auth A] MOL2 format, chain HA [auth F] MOL2 format, chain FA [auth E] MOL2 format, chain BA [auth E] mmCIF format, chain X [auth D] mmCIF format, chain S [auth B] mmCIF format, chain OA [auth G] mmCIF format, chain O [auth B] mmCIF format, chain K [auth A] mmCIF format, chain HA [auth F] mmCIF format, chain FA [auth E] mmCIF format, chain BA [auth E]	BA [auth E] FA [auth E] HA [auth F] K [auth A] O [auth B] BA [auth E], FA [auth E], HA [auth F], K [auth A], O [auth B], OA [auth G], S [auth B], X [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain FA [auth E] Focus chain HA [auth F] Focus chain K [auth A] Focus chain O [auth B] Focus chain OA [auth G] Focus chain S [auth B] Focus chain X [auth D] Interactions & Density Focus chain BA [auth E] Focus chain FA [auth E] Focus chain HA [auth F] Focus chain K [auth A] Focus chain O [auth B] Focus chain OA [auth G] Focus chain S [auth B] Focus chain X [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain M [auth A] SDF format, chain LA [auth F] SDF format, chain KA [auth F] SDF format, chain EA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain KA [auth F] MOL2 format, chain EA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain KA [auth F] mmCIF format, chain EA [auth E]	EA [auth E] KA [auth F] LA [auth F] M [auth A] Q [auth B] EA [auth E], KA [auth F], LA [auth F], M [auth A], Q [auth B], R [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain EA [auth E] Focus chain KA [auth F] Focus chain LA [auth F] Focus chain M [auth A] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain EA [auth E] Focus chain KA [auth F] Focus chain LA [auth F] Focus chain M [auth A] Focus chain Q [auth B] Focus chain R [auth B]