6MRO | pdb_00006mro

Crystal structure of methyl transferase from Methanosarcina acetivorans at 1.6 Angstroms resolution, Northeast Structural Genomics Consortium (NESG) Target MvR53.

PDB DOI: https://doi.org/10.2210/pdb6MRO/pdb

Classification: TRANSFERASE
Organism(s): Methanosarcina acetivorans C2A
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2018-10-15 Released: 2018-10-24
Deposition Author(s): Singh, S., Forouhar, F., Wang, C., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.210 (Depositor), 0.208 (DCC)
R-Value Work:
0.179 (Depositor), 0.186 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of a methyl transferase from Methanosarcina acetivorans at 1.6 Angstroms resolution.

Singh, S., Forouhar, F., Wang, C., Vorobiev, S.M., Neky, M.J., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 22.74 kDa
Atom Count: 1,801
Modeled Residue Count: 194
Deposited Residue Count: 194
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
methyl transferase from Methanosarcina acetivorans	A	194	Methanosarcina acetivorans C2A	Mutation(s): 1 Gene Names: MA_2137
UniProt
Find proteins for Q8TNZ0 (Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)) Explore Q8TNZ0 Go to UniProtKB: Q8TNZ0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TNZ0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH 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]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.210 (Depositor), 0.208 (DCC)
R-Value Work: 0.179 (Depositor), 0.186 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.99	α = 90
b = 40.99	β = 90
c = 104.85	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-10-24

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2018-10-24
Type: Initial release
Version 1.1: 2018-10-31
Changes: Data collection, Database references
Version 1.2: 2018-11-14
Changes: Data collection, Structure summary
Version 1.3: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description

6MRO | pdb_00006mro

Crystal structure of methyl transferase from Methanosarcina acetivorans at 1.6 Angstroms resolution, Northeast Structural Genomics Consortium (NESG) Target MvR53.

Literature

Crystal structure of a methyl transferase from Methanosarcina acetivorans at 1.6 Angstroms resolution.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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