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 1.2 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: 1MDZ, 1MDO, 1MDX, 1VJE, 1VIO, 1VI7, 1VHN, 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
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
A, B, C, D, E, F
170Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)Mutation(s): 0 
Gene Names: ispF
EC: 4.6.1.12
Find proteins for P44815 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Go to UniProtKB:  P44815
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POP
Query on POP

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

Download SDF File 
Download CCD File 
A, B, C, D, E, F
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
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 = 104.850α = 90.00
b = 104.850β = 90.00
c = 195.750γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling

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