1VH8

Crystal structure of a 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.240 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1002/prot.20541
  • Primary Citation of Related Structures:  
    1O60, 1O61, 1O62, 1O63, 1O64, 1O65, 1O66, 1O67, 1O68, 1O69, 1O6B, 1O6C, 1O6D, 1VGT, 1VGU, 1VGV, 1VGW, 1VGX, 1VGY, 1VGZ, 1VH0, 1VH1, 1VH2, 1VH3, 1VH4, 1VH5, 1VH6, 1VH7, 1VH8, 1VH9, 1VHA, 1VHC, 1VHD, 1VHE, 1VHF, 1VHG, 1VHJ, 1VHK, 1VHL, 1VHM, 1VHO, 1VHQ, 1VHS, 1VHT, 1VHU, 1VHV, 1VHW, 1VHX, 1VHY, 1VHZ

  • 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, 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
A, B, C, D, E
A, B, C, D, E, F
170Haemophilus influenzaeMutation(s): 3 
Gene Names: ISPFHI0671
EC: 4.6.1.12
UniProt
Find proteins for P44815 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Explore P44815 
Go to UniProtKB:  P44815
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP44815
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.240 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.85α = 90
b = 104.85β = 90
c = 195.75γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-12-30
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations