4DPO | pdb_00004dpo

Crystal structure of a conserved protein MM_1583 from Methanosarcina mazei Go1

• PDB DOI: https://doi.org/10.2210/pdb4DPO/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Methanosarcina mazei Go1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-02-13 Released: 2012-02-29 
• Deposition Author(s): Agarwal, R., Chamala, S., Evans, R., Gizzi, A., Hillerich, B., Kar, A., LaFleur, J., Foti, R., Siedel, R., Zencheck, W., Villigas, G., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.73 Å
• R-Value Free: 
  0.283 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.247 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Literature

Crystal structure of a conserved protein MM_1583 from Methanosarcina mazei Go1

Agarwal, R., Almo, S.C., Swaminathan, S.

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: 28.5 kDa 
• Atom Count: 1,554 
• Modeled Residue Count: 203 
• Deposited Residue Count: 238 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Conserved protein	A, B	119	Methanosarcina mazei Go1	Mutation(s): 0  Gene Names: MM_1583
UniProt
Find proteins for Q8PWK2 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)) Explore Q8PWK2  Go to UniProtKB:  Q8PWK2

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.73 Å
• R-Value Free:  0.283 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.247 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.761	α = 90
b = 60.255	β = 90
c = 104.312	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
AutoSol	phasing
Coot	model building
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-29 
Deposition Author(s): Agarwal, R., Chamala, S., Evans, R., Gizzi, A., Hillerich, B., Kar, A., LaFleur, J., Foti, R., Siedel, R., Zencheck, W., Villigas, G., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2012-02-29
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary