1VHE

Crystal structure of a aminopeptidase/glucanase homolog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural analysis of a set of proteins resulting from a bacterial genomics project

Badger, J.Sauder, J.M.Adams, J.M.Antonysamy, S.Bain, K.Bergseid, M.G.Buchanan, S.G.Buchanan, M.D.Batiyenko, Y.Christopher, J.A.Emtage, S.Eroshkina, A.Feil, I.Furlong, E.B.Gajiwala, K.S.Gao, X.He, D.Hendle, J.Huber, A.Hoda, K.Kearins, P.Kissinger, C.Laubert, B.Lewis, H.A.Lin, J.Loomis, K.Lorimer, D.Louie, G.Maletic, M.Marsh, C.D.Miller, I.Molinari, J.Muller-Dieckmann, H.J.Newman, J.M.Noland, B.W.Pagarigan, B.Park, F.Peat, T.S.Post, K.W.Radojicic, S.Ramos, A.Romero, R.Rutter, M.E.Sanderson, W.E.Schwinn, K.D.Tresser, J.Winhoven, J.Wright, T.A.Wu, L.Xu, J.Harris, T.J.

(2005) Proteins 60: 787-796

  • DOI: 10.1002/prot.20541
  • Primary Citation of Related Structures:  
  • Also Cited By: 1VJE, 1VIO, 1VI7, 1VHN, 1MDZ, 1MDX, 1MDO, 1J6X, 1J6W, 1J6V, 1INN

  • PubMed Abstract: 
  • The targets of the Structural GenomiX (SGX) bacterial genomics project were proteins conserved in multiple prokaryotic organisms with no obvious sequence homolog in the Protein Data Bank of known structures. The outcome of this work was 80 structures ...

    The targets of the Structural GenomiX (SGX) bacterial genomics project were proteins conserved in multiple prokaryotic organisms with no obvious sequence homolog in the Protein Data Bank of known structures. The outcome of this work was 80 structures, covering 60 unique sequences and 49 different genes. Experimental phase determination from proteins incorporating Se-Met was carried out for 45 structures with most of the remainder solved by molecular replacement using members of the experimentally phased set as search models. An automated tool was developed to deposit these structures in the Protein Data Bank, along with the associated X-ray diffraction data (including refined experimental phases) and experimentally confirmed sequences. BLAST comparisons of the SGX structures with structures that had appeared in the Protein Data Bank over the intervening 3.5 years since the SGX target list had been compiled identified homologs for 49 of the 60 unique sequences represented by the SGX structures. This result indicates that, for bacterial structures that are relatively easy to express, purify, and crystallize, the structural coverage of gene space is proceeding rapidly. More distant sequence-structure relationships between the SGX and PDB structures were investigated using PDB-BLAST and Combinatorial Extension (CE). Only one structure, SufD, has a truly unique topology compared to all folds in the PDB.


    Organizational Affiliation

    Structural GenomiX Inc., San Diego, California, USA. jbadger@active-sight.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
aminopeptidase/glucanase homolog
A
373Bacillus subtilis (strain 168)Gene Names: ysdC
EC: 3.4.11.-
Find proteins for P94521 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P94521
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.176 
  • Space Group: F 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 223.966α = 90.00
b = 223.966β = 90.00
c = 223.966γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2003-12-01 
  • Released Date: 2003-12-30 
  • Deposition Author(s): Structural GenomiX

Revision History 

  • Version 1.0: 2003-12-30
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance