2A6A | pdb_00002a6a

Crystal structure of Glycoprotein endopeptidase (tm0874) from THERMOTOGA MARITIMA at 2.50 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.235 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.193 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2A6A

This is version 1.4 of the entry. See complete history. 

Literature

Structure of an essential bacterial protein YeaZ (TM0874) from Thermotoga maritima at 2.5 A resolution.

Xu, Q., McMullan, D., Jaroszewski, L., Krishna, S.S., Elsliger, M.A., Yeh, A.P., Abdubek, P., Astakhova, T., Axelrod, H.L., Carlton, D., Chiu, H.J., Clayton, T., Duan, L., Feuerhelm, J., Grant, J., Han, G.W., Jin, K.K., Klock, H.E., Knuth, M.W., Miller, M.D., Morse, A.T., Nigoghossian, E., Okach, L., Oommachen, S., Paulsen, J., Reyes, R., Rife, C.L., van den Bedem, H., Hodgson, K.O., Wooley, J., Deacon, A.M., Godzik, A., Lesley, S.A., Wilson, I.A.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 1230-1236

  • DOI: https://doi.org/10.1107/S1744309109022192
  • Primary Citation Related Structures: 
    2A6A

  • PubMed Abstract: 

    YeaZ is involved in a protein network that is essential for bacteria. The crystal structure of YeaZ from Thermotoga maritima was determined to 2.5 Å resolution. Although this protein belongs to a family of ancient actin-like ATPases, it appears that it has lost the ability to bind ATP since it lacks some key structural features that are important for interaction with ATP. A conserved surface was identified, supporting its role in the formation of protein complexes.

    • Organizational Affiliation: 
    • Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 49.25 kDa 
  • Atom Count: 2,889 
  • Modeled Residue Count: 381 
  • Deposited Residue Count: 436 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
hypothetical protein TM0874
A, B
218Thermotoga maritima MSB8Mutation(s): 3 
Gene Names: tm0874
UniProt
Find proteins for Q9WZX7 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9WZX7 
Go to UniProtKB:  Q9WZX7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WZX7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UNL

Query on UNL


Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]		Unknown ligand
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.235 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.193 (DCC) 
Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.272α = 90
b = 217.112β = 90
c = 51.953γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
CCP4data scaling
SHELXDphasing
autoSHARPphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-07-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.3: 2023-01-25
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-11-13
    Changes: Data collection, Refinement description, Structure summary