2IEC

Crystal Structure of uncharacterized conserved archael protein from Methanopyrus kandleri

• PDB DOI: https://doi.org/10.2210/pdb2IEC/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Methanopyrus kandleri
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-09-18 Released: 2006-10-03 
• Deposition Author(s): Bonanno, J.B., Ramagopal, U.A., Dickey, M., Bain, K.T., Powell, A., Ozyurt, S., Wasserman, S., Sauder, J.M., 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: 2.33 Å
• R-Value Free: 
  0.295 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of uncharacterized conserved archael protein from Methanopyrus kandleri

Bonanno, J.B., Ramagopal, U.A., Dickey, M., Bain, K.T., Powell, A., Ozyurt, S., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 59.91 kDa 
• Atom Count: 3,824 
• Modelled Residue Count: 455 
• Deposited Residue Count: 524 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein conserved in archaea	A, B, C, D	131	Methanopyrus kandleri	Mutation(s): 0  Gene Names: Q8TX89_METKA, MK0786 EC: 4.1.2.25
UniProt
Find proteins for Q8TX89 (Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)) Explore Q8TX89  Go to UniProtKB:  Q8TX89

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth B], F [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free:  0.295 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.833	α = 90
b = 60.833	β = 90
c = 263.945	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
DENZO	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-03 
Deposition Author(s): Bonanno, J.B., Ramagopal, U.A., Dickey, M., Bain, K.T., Powell, A., Ozyurt, S., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2006-10-03
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Advisory, Refinement description
• Version 1.4: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.5: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.6: 2023-08-30
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 1.7: 2024-11-13
  Changes: Structure summary