4YQY

Crystal Structure of a putative Dehydrogenase from Sulfitobacter sp. (COG1028) (TARGET EFI-513936) in its APO form

PDB DOI: https://doi.org/10.2210/pdb4YQY/pdb

Classification: OXIDOREDUCTASE
Organism(s): Sulfitobacter sp. NAS-14.1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2015-03-13 Released: 2015-03-25
Deposition Author(s): Yadava, U., Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Koss, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.38 Å
R-Value Free: 0.186
R-Value Work: 0.173
R-Value Observed: 0.174

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of a putative Dehydrogenase from Sulfitobacter sp. (COG1028, TARGET EFI-513936) in its APO form

Yadava, U., Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Koss, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Macromolecule Content

Total Structure Weight: 57.72 kDa
Atom Count: 3,959
Modelled Residue Count: 484
Deposited Residue Count: 540
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative Dehydrogenase	A, B	270	Sulfitobacter sp. NAS-14.1	Mutation(s): 2 Gene Names: NAS141_03711
UniProt
Find proteins for A3T0C9 (Sulfitobacter sp. (strain NAS-14.1)) Explore A3T0C9 Go to UniProtKB: A3T0C9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3T0C9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B]	C [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.38 Å
R-Value Free: 0.186
R-Value Work: 0.173
R-Value Observed: 0.174
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.795	α = 90
b = 84.795	β = 90
c = 126.16	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2015-03-25

Deposition Author(s):

Al Obaidi, N.F.

Wasserman, S.R.

Scott Glenn, A.

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2015-03-25
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.