1NMP | pdb_00001nmp

Structural genomics, ybgI protein, unknown function

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.253 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history. 

Literature

Crystal Structure of Escherichia coli Protein ybgI, a toroidal structure with a dinuclear metal site

Ladner, J.E., Obmolova, G., Teplyakov, A., Howard, A.J., Khil, P.P., Camerini-Otero, R.D., Gilliland, G.L.

(2003) BMC Struct Biol 3: 7

  • DOI: https://doi.org/10.1186/1472-6807-3-7
  • Primary Citation Related Structures: 
    1LQA, 1NMO, 1NMP

  • PubMed Abstract: 

    The protein encoded by the gene ybgI was chosen as a target for a structural genomics project emphasizing the relation of protein structure to function. The structure of the ybgI protein is a toroid composed of six polypeptide chains forming a trimer of dimers. Each polypeptide chain binds two metal ions on the inside of the toroid. The toroidal structure is comparable to that of some proteins that are involved in DNA metabolism. The di-nuclear metal site could imply that the specific function of this protein is as a hydrolase-oxidase enzyme.

    • Organizational Affiliation: 
    • Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA. jane.ladner@nist.gov

Macromolecule Content 

  • Total Structure Weight: 161.78 kDa 
  • Atom Count: 11,969 
  • Modeled Residue Count: 1,482 
  • Deposited Residue Count: 1,482 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hypothetical protein ybgI
A, B, C, D, E
A, B, C, D, E, F
247Escherichia coli, Escherichia coli O157:H7
This entity is chimeric		Mutation(s): 0 
Gene Names: YBGI OR B0710 OR Z0861 OR ECS0735
UniProt
Find proteins for P0AFP6 (Escherichia coli (strain K12))
Explore P0AFP6 
Go to UniProtKB:  P0AFP6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AFP6
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on MG


Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth B]
J [auth C]
K [auth C]
G [auth A],
H [auth A],
I [auth B],
J [auth C],
K [auth C],
L [auth D],
M [auth D],
N [auth E],
O [auth E],
P [auth F],
Q [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.253 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.73α = 90
b = 156.73β = 90
c = 57.61γ = 120
Software Package:
Software NamePurpose
MAR345data collection
d*TREKdata reduction
CNSrefinement
d*TREKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-01-20
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations
  • Version 1.5: 2024-04-03
    Changes: Refinement description