3DA1 | pdb_00003da1

X-Ray structure of the glycerol-3-phosphate dehydrogenase from Bacillus halodurans complexed with FAD. Northeast Structural Genomics Consortium target BhR167.

PDB DOI: https://doi.org/10.2210/pdb3DA1/pdb

Classification: OXIDOREDUCTASE
Organism(s): Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Mutation(s): No

Deposited: 2008-05-28 Released: 2008-07-29
Deposition Author(s): Kuzin, A.P., Abashidze, M., Seetharaman, J., Wang, D., Janjua, H., Owens, L., Xiao, R., Nair, R., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.282 (Depositor), 0.291 (DCC)
R-Value Work:
0.222 (Depositor), 0.230 (DCC)
R-Value Observed:
0.222 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

X-Ray structure of the glycerol-3-phosphate dehydrogenase from Bacillus halodurans complexed with FAD. Northeast Structural Genomics Consortium target BhR167.

Kuzin, A.P., Abashidze, M., Seetharaman, J., Wang, D., Janjua, H., Owens, L., Xiao, R., Nair, R., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 64.68 kDa
Atom Count: 4,005
Modeled Residue Count: 496
Deposited Residue Count: 561
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerol-3-phosphate dehydrogenase	A	561	N/A	Mutation(s): 0 EC: 1.1.5.3
UniProt
Find proteins for Q9KDW6 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Explore Q9KDW6 Go to UniProtKB: Q9KDW6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KDW6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD 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]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.282 (Depositor), 0.291 (DCC)
R-Value Work: 0.222 (Depositor), 0.230 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.767	α = 90
b = 96.953	β = 90
c = 226.057	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-07-29

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2008-07-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary