3KHK | pdb_00003khk

Crystal structure of type-I restriction-modification system methylation subunit (MM_0429) from Methanosarchina mazei.

PDB DOI: https://doi.org/10.2210/pdb3KHK/pdb

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

Deposited: 2009-10-30 Released: 2010-01-19
Deposition Author(s): Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free:
0.242 (Depositor), 0.234 (DCC)
R-Value Work:
0.213 (Depositor), 0.209 (DCC)
R-Value Observed:
0.214 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3KHK

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

Literature

Crystal structure of type-I restriction-modification system methylation subunit (MM_0429) from Methanosarchina mazei.

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

To be published.

Macromolecule Content

Total Structure Weight: 125.92 kDa
Atom Count: 7,891
Modeled Residue Count: 975
Deposited Residue Count: 1,088
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type I restriction-modification system methylation subunit	A, B	544	Methanosarcina mazei	Mutation(s): 0 Gene Names: MM_0429 EC: 2.1.1.72
UniProt
Find proteins for Q8PZR3 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)) Explore Q8PZR3 Go to UniProtKB: Q8PZR3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8PZR3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.242 (Depositor), 0.234 (DCC)
R-Value Work: 0.213 (Depositor), 0.209 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.648	α = 90
b = 80.648	β = 90
c = 179.973	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing
SHELXD	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-01-19

Deposition Author(s):

Ramagopal, U.A.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2010-01-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
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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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.