4IYM Oxidoreductase date Jan 28, 2013
title Crystal Structure Of Putative Methylmalonate-Semialdehyde Dehydrogenase From Sinorhizobium Meliloti 1021 Complexed Wi Target 011934
authors V.N.Malashkevich, R.Bhosle, R.Toro, B.Hillerich, A.Gizzi, S.Garfo A.Kar, M.K.Chan, J.Lafluer, H.Patel, B.Matikainen, S.Chamala, S.L A.Celikgil, G.Villegas, B.Evans, W.Zenchek, J.Love, A.Fiser, K.Kh R.Seidel, J.B.Bonanno, S.C.Almo, New York Structural Genomics Consortium (Nysgrc)
compound source
Molecule: Methylmalonate-Semialdehyde Dehydrogenase
Chain: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
Ec: 1.2.1.27
Engineered: Yes
Organism_scientific: Sinorhizobium Meliloti
Organism_common: Ensifer Meliloti
Organism_taxid: 266834
Strain: 1021
Gene: Iola, Mmsa, R00726, Smc00781
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)Codon+Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Bc-Psgx3(Bc)
symmetry Space Group: P 1 21 1
R_factor 0.165 R_Free 0.209
crystal
cell
length a length b length c angle alpha angle beta angle gamma
159.472 170.910 170.466 90.00 106.33 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand MG, MSE, NAD enzyme Oxidoreductase E.C.1.2.1.27 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, N, K, E, M, C, L, A, J, O, P, B, H, D, I, G


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2554 Kb) [Save to disk]
  • Biological Unit Coordinates (4iym.pdb1.gz) 643 Kb
  • Biological Unit Coordinates (4iym.pdb2.gz) 645 Kb
  • Biological Unit Coordinates (4iym.pdb3.gz) 647 Kb
  • Biological Unit Coordinates (4iym.pdb4.gz) 644 Kb
  • LPC: Ligand-Protein Contacts for 4IYM
  • CSU: Contacts of Structural Units for 4IYM
  • Structure Factors (9852 Kb)
  • Retrieve 4IYM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4IYM from S2C, [Save to disk]
  • Re-refined 4iym structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4IYM in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4IYM
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4IYM, from MSDmotif at EBI
  • Fold representative 4iym from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4iym_M] [4iym_A] [4iym_K] [4iym_E] [4iym_B] [4iym_P] [4iym_N] [4iym_G] [4iym_I] [4iym_F] [4iym_J] [4iym_H] [4iym_C] [4iym] [4iym_D] [4iym_O] [4iym_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4IYM
  • Community annotation for 4IYM at PDBWiki (http://pdbwiki.org)

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