3DTN

Crystal structure of putative Methyltransferase-MM_2633 from Methanosarcina mazei .

PDB DOI: https://doi.org/10.2210/pdb3DTN/pdb

Classification: structural genomics, unknown function
Organism(s): Methanosarcina mazei
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-07-15 Released: 2008-09-09
Deposition Author(s): Ramagopal, U.A., Toro, R., Meyer, A.J., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.234
R-Value Work: 0.187
R-Value Observed: 0.189

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of putative Methyltransferase-MM_2633 from Methanosarcina mazei

Ramagopal, U.A., Toro, R., Meyer, A.J., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 54.83 kDa
Atom Count: 3,656
Modelled Residue Count: 433
Deposited Residue Count: 468
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative Methyltransferase MM_2633	A, B	234	Methanosarcina mazei	Mutation(s): 0 Gene Names: MM_2633
UniProt
Find proteins for Q8PTS9 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)) Explore Q8PTS9 Go to UniProtKB: Q8PTS9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8PTS9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B]	D [auth A], F [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.234
R-Value Work: 0.187
R-Value Observed: 0.189
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.276	α = 90
b = 49.94	β = 108.17
c = 77.512	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SHELXD	phasing
SHELXE	model building
CCP4	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-09-09

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2008-09-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-02-21
Changes: Data collection, Database references

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Help and Resources

3DTN

Crystal structure of putative Methyltransferase-MM_2633 from Methanosarcina mazei .

Crystal structure of putative Methyltransferase-MM_2633 from Methanosarcina mazei

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)