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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.242 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

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

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.242 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.210 (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

Entry History 

Deposition Data

• Released Date: 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)

Revision History  

• 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