1ZXJ | pdb_00001zxj

Crystal structure of the hypthetical Mycoplasma protein, MPN555


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.322 (Depositor), 0.321 (DCC) 
  • R-Value Work: 
    0.248 (Depositor), 0.251 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1ZXJ

This is version 1.4 of the entry. See complete history

Literature

Structure of the hypothetical Mycoplasma protein MPN555 suggests a chaperone function.

Schulze-Gahmen, U.Aono, S.Chen, S.Yokota, H.Kim, R.Kim, S.H.

(2005) Acta Crystallogr D Biol Crystallogr 61: 1343-1347

  • DOI: https://doi.org/10.1107/S090744490502264X
  • Primary Citation Related Structures: 
    1ZXJ

  • PubMed Abstract: 

    The crystal structure of the hypothetical protein MPN555 from Mycoplasma pneumoniae (gi|1673958) has been determined to a resolution of 2.8 Angstrom using anomalous diffraction data at the Se-peak wavelength. Structure determination revealed a mostly alpha-helical protein with a three-lobed shape. The three lobes or fingers delineate a central binding groove and additional grooves between lobes 1 and 3 and between lobes 2 and 3. For one of the molecules in the asymmetric unit, the central binding pocket was filled with a peptide from the uncleaved N-terminal affinity tag. The MPN555 structure has structural homology to two bacterial chaperone proteins: SurA and trigger factor from Escherichia coli. The structural data and the homology to other chaperone proteins suggests an involvement in protein folding as a molecular chaperone for MPN555.


  • Organizational Affiliation
    • Berkeley Structural Genomics Center, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.

Macromolecule Content 

  • Total Structure Weight: 101.81 kDa 
  • Atom Count: 5,910 
  • Modeled Residue Count: 748 
  • Deposited Residue Count: 872 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hypothetical protein MG377 homolog
A, B, C, D
218Mycoplasmoides pneumoniaeMutation(s): 0 
UniProt
Find proteins for P75223 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
Explore P75223 
Go to UniProtKB:  P75223
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP75223
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.322 (Depositor), 0.321 (DCC) 
  • R-Value Work:  0.248 (Depositor), 0.251 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.37α = 90
b = 45.59β = 111.4
c = 153.93γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-07-26
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references