5VIP Transferase date Apr 17, 2017
title Crystal Structure Of Pseudomonas Malonate Decarboxylase Mdcd Hetero-Dimer
authors R.Maderbocus, L.Tong
compound source
Molecule: Mdce
Chain: A, C
Synonym: Biotin-Independent Malonate Decarboxylase Subunit
Malonate Decarboxylase,Gamma Subunit,Malonyl-S-Acp: Biotin-P Carboxyltransferase Madd;
Ec: 2.1.3.10
Engineered: Yes
 Organism_scientific: Pseudomonas Aeruginosa
Organism_taxid: 287
Gene: Madd, Ao964_31595, Aoy09_06293, Paerug_e15_london_28_01_14_07062, Paerug_p32_london_17_vim_2_10_11_04128;
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Mdcd
Chain: B, D
Synonym: Biotin-Independent Malonate Decarboxylase Subunit
Malonate Decarboxylase Subunit Beta,Malonyl-S-Acp: Biotin-Pr Carboxyltransferase Madc,Methylmalonyl-Coa Carboxyltransfer Subunit;
Ec: 2.1.3.10,2.1.3.1
Engineered: Yes
Organism_scientific: Pseudomonas Aeruginosa
Organism_taxid: 287
Gene: Madc, Mdcd, Ao964_31600, Aoy09_06294, Bh593_13640, Paerug_e15_london_28_01_14_07061, Paerug_p32_london_17_vim_2_10_11_04127, Pamh19_0209;
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor 0.181 R_Free 0.208
crystal
cell
length a length b length c angle alpha angle beta angle gamma
56.310 60.076 91.277 89.87 88.77 68.80
method X-Ray Diffractionresolution 1.86 Å
ligand MSE enzyme Transferase E.C.2.1.3.10 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


Primary referenceCrystal structure of a Pseudomonas malonate decarboxylase holoenzyme hetero-tetramer., Maderbocus R, Fields BL, Hamilton K, Luo S, Tran TH, Dietrich LEP, Tong L, Nat Commun. 2017 Jul 31;8(1):160. doi: 10.1038/s41467-017-00233-z. PMID:28757619
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (161 Kb) [Save to disk]
  • Biological Unit Coordinates (5vip.pdb1.gz) 75 Kb
  • Biological Unit Coordinates (5vip.pdb2.gz) 83 Kb
  • LPC: Ligand-Protein Contacts for 5VIP
  • CSU: Contacts of Structural Units for 5VIP
  • Structure Factors (1323 Kb)
  • Retrieve 5VIP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VIP from S2C, [Save to disk]
    • View 5VIP 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 5VIP
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vip_B] [5vip_A] [5vip_C] [5vip_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5VIP
  • Community annotation for 5VIP at PDBWiki (http://pdbwiki.org)

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