3DTN | pdb_00003dtn

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.234 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

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

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	D [auth A], F [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	C [auth A], E [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.234 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

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

Entry History 

Deposition Data

• Released Date: 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)

Revision History  

• 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