3MGG | pdb_00003mgg

Crystal Structure of Methyl Transferase from Methanosarcina mazei

PDB DOI: https://doi.org/10.2210/pdb3MGG/pdb

Classification: TRANSFERASE
Organism(s): Methanosarcina mazei
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-04-06 Released: 2010-04-21
Deposition Author(s): Syed Ibrahim, B., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.239 (Depositor), 0.241 (DCC)
R-Value Work:
0.214 (Depositor), 0.214 (DCC)
R-Value Observed:
0.214 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3MGG

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Methyl Transferase from Methanosarcina mazei

Syed Ibrahim, B., Burley, S.K., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 62.93 kDa
Atom Count: 4,238
Modeled Residue Count: 499
Deposited Residue Count: 552
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyltransferase	A, B	276	Methanosarcina mazei	Mutation(s): 0 Gene Names: MM_1949 EC: 2.1.1
UniProt
Find proteins for Q8PVL4 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)) Explore Q8PVL4 Go to UniProtKB: Q8PVL4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8PVL4
Sequence Annotations Expand
Reference Sequence

Small Molecules

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: 1.86 Å
R-Value Free: 0.239 (Depositor), 0.241 (DCC)
R-Value Work: 0.214 (Depositor), 0.214 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.805	α = 90
b = 56.019	β = 90
c = 234.607	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELX	model building
SHARP	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-04-21

Deposition Author(s):

Syed Ibrahim, B.

Swaminathan, S.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2010-04-21
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Structure summary

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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.