3EZX | pdb_00003ezx

Structure of Methanosarcina barkeri monomethylamine corrinoid protein

PDB DOI: https://doi.org/10.2210/pdb3EZX/pdb

Classification: TRANSFERASE
Organism(s): Methanosarcina barkeri
Mutation(s): No

Deposited: 2008-10-23 Released: 2009-12-15
Deposition Author(s): Jain, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.56 Å
R-Value Free:
0.262 (Depositor), 0.263 (DCC)
R-Value Work:
0.205 (Depositor)
R-Value Observed:
0.205 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Structure of Methanosarcina barkeri monomethylamine corrinoid protein

Jain, R., Hao, B., Soares, J.A., Zhang, L., Green-Church, K., Li, X., Krzycki, J.A., Chan, M.K.

To be published.

Macromolecule Content

Total Structure Weight: 24.3 kDa
Atom Count: 1,764
Modeled Residue Count: 212
Deposited Residue Count: 215
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Monomethylamine corrinoid protein 1	A	215	Methanosarcina barkeri	Mutation(s): 0
UniProt
Find proteins for O30641 (Methanosarcina barkeri) Explore O30641 Go to UniProtKB: O30641
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O30641
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HCB Query on HCB 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]	5-HYDROXYBENZIMIDAZOLYLCOBAMIDE C₆₀ H₈₄ Co N₁₃ O₁₅ P LQBVMYRJXRYHOO-NCVPRIERSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.56 Å
R-Value Free: 0.262 (Depositor), 0.263 (DCC)
R-Value Work: 0.205 (Depositor)
R-Value Observed: 0.205 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.97	α = 90
b = 77.71	β = 90
c = 100.36	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-12-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-12-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-12-27
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.