1VHA

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.244 

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:  
    1O67, 1O66, 1O65, 1O64, 1O63, 1O62, 1O61, 1O60, 1O69, 1O68

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthaseABCDEF170Haemophilus influenzaeMutation(s): 3 
Gene Names: ispFHI0671
EC: 4.6.1.12
Find proteins for P44815 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Explore P44815 
Go to UniProtKB:  P44815
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POP
Query on POP

Download CCD File 
B, D
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
ACY
Query on ACY

Download CCD File 
A, B, C, D, E, F
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download CCD File 
A, B, C, D, F
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,B,C,D,E,FL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.244 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.715α = 90
b = 104.715β = 90
c = 195.864γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report



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
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance