2WNY | pdb_00002wny

Structure of Mth689, a DUF54 protein from Methanothermobacter thermautotrophicus

• PDB DOI: https://doi.org/10.2210/pdb2WNY/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Methanothermobacter thermautotrophicus
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2009-07-21 Released: 2010-09-01 
• Deposition Author(s): Ng, C.L., Waterman, D.G., Lebedev, A.A., Smits, C., Ortiz-Lombardia, M., Antson, A.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.247 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Structure of Mth689, a Duf54 Protein from Methanothermobacter Thermautotrophicus

Ng, C.L., Waterman, D.G., Lebedev, A.A., Smits, C., Ortiz-Lombardia, M., Antson, A.A.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 33.11 kDa 
• Atom Count: 2,467 
• Modeled Residue Count: 273 
• Deposited Residue Count: 282 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CONSERVED PROTEIN MTH689	A, B	141	Methanothermobacter thermautotrophicus	Mutation(s): 1
UniProt
Find proteins for O26785 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O26785  Go to UniProtKB:  O26785

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CL	D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.247 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.576	α = 90
b = 61.021	β = 90
c = 88.311	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-01 
Deposition Author(s): Ng, C.L., Waterman, D.G., Lebedev, A.A., Smits, C., Ortiz-Lombardia, M., Antson, A.A.

Revision History  

• Version 1.0: 2010-09-01
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description