3KA7 | pdb_00003ka7

Crystal Structure of an oxidoreductase from Methanosarcina mazei. Northeast Structural Genomics Consortium target id MaR208

PDB DOI: https://doi.org/10.2210/pdb3KA7/pdb

Classification: OXIDOREDUCTASE
Organism(s): Methanosarcina mazei
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-10-18 Released: 2009-11-17
Deposition Author(s): Seetharaman, J., Su, M., Wang, D., Janjua, H., Cunningham, K., Owens, L., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.223 (Depositor), 0.230 (DCC)
R-Value Work:
0.194 (Depositor)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of an oxidoreductase from Methanosarcina mazei

Seetharaman, J., Su, M., Sahdev, S., Janjua, H., Xiao, R., Ciccosanti, C., Foote, E.L., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 46.88 kDa
Atom Count: 3,598
Modeled Residue Count: 422
Deposited Residue Count: 425
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase	A	425	Methanosarcina mazei	Mutation(s): 0 Gene Names: MM_2493
UniProt
Find proteins for Q8PU56 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)) Explore Q8PU56 Go to UniProtKB: Q8PU56
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8PU56
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: 1.80 Å
R-Value Free: 0.223 (Depositor), 0.230 (DCC)
R-Value Work: 0.194 (Depositor)
R-Value Observed: 0.195 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.178	α = 90
b = 67.182	β = 90
c = 128.074	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SHELXS	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-11-17

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2009-11-17
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