3R6A | pdb_00003r6a

Crystal structure of an uncharacterized protein (hypothetical protein MM_3218) from Methanosarcina mazei.

PDB DOI: https://doi.org/10.2210/pdb3R6A/pdb

Classification: isomerase, lyase
Organism(s): Methanosarcina mazei Go1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-03-21 Released: 2011-04-06
Deposition Author(s): Eswaramoorthy, S., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.234 (Depositor), 0.234 (DCC)
R-Value Work:
0.218 (Depositor), 0.218 (DCC)
R-Value Observed:
0.218 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3R6A

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

Literature

Crystal structure of an uncharacterized protein (hypothetical protein MM_3218) from Methanosarcina mazei.

Eswaramoorthy, S., Almo, S.C., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 33.59 kDa
Atom Count: 2,015
Modeled Residue Count: 241
Deposited Residue Count: 288
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	144	Methanosarcina mazei Go1	Mutation(s): 0 Gene Names: Glo_EDI_BRP_like, MM_3218 EC: 4.4.1.5
UniProt
Find proteins for Q8PS64 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)) Explore Q8PS64 Go to UniProtKB: Q8PS64
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8PS64
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

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: 1.76 Å
R-Value Free: 0.234 (Depositor), 0.234 (DCC)
R-Value Work: 0.218 (Depositor), 0.218 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.433	α = 90
b = 62.433	β = 90
c = 149.595	γ = 120

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-04-06

Deposition Author(s):

Eswaramoorthy, S.

Swaminathan, S.

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2011-04-06
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

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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.