3IAB Hydrolase Rna date Jul 13, 2009
title Crystal Structure Of Rnase P Rnase Mrp Proteins Pop6, Pop7 In A Complex With The P3 Domain Of Rnase Mrp Rna
authors A.Perederina, O.A.Esakova, C.Quan, E.Khanova, A.S.Krasilnikov
compound source
Molecule: Ribonucleases Pmrp Protein Subunit Pop6
Chain: A
Fragment: Pop6
Synonym: Rna-Processing Protein Pop6, Rnases Pmrp 18.2 Kda Subunit;
Ec: 3.1.26.5
Engineered: Yes
Mutation: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
Gene: Pop6, Ygr030c
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl-21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: 762

Molecule: Ribonucleases Pmrp Protein Subunit Pop7
Chain: B
Fragment: Pop7
Synonym: Rna-Processing Protein Pop7, Rnases Pmrp 15.8 Kda Subunit;
Ec: 3.1.26.5
Engineered: Yes
Mutation: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
Gene: Pop7, Rpp2, Ybr1219, Ybr167c
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl-21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: 762

Molecule: P3 Domain Of The Rna Component Of Rnase Mrp
Chain: R
Fragment: P3 Domain
Ec: 3.1.26.5
Engineered: Yes
Mutation: Yes

Synthetic: Yes
Other_details: In Vitro Transcription; Circular Permutation Of Naturally Occurring Sequence.
symmetry Space Group: P 42 2 2
R_factor 0.250 R_Free 0.265
crystal
cell
length a length b length c angle alpha angle beta angle gamma
126.514 126.514 76.766 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand MSE, ZN enzyme Hydrolase E.C.3.1.26.5 BRENDA
note 3IAB is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A
  • ribonuclease MRP activity
  • ribonuclease P activity


  • B
  • ribonuclease MRP activity
  • ribonuclease P activity


  • Primary referenceEukaryotic ribonucleases P/MRP: the crystal structure of the P3 domain., Perederina A, Esakova O, Quan C, Khanova E, Krasilnikov AS, EMBO J. 2010 Jan 14. PMID:20075859
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (69 Kb) [Save to disk]
  • Biological Unit Coordinates (3iab.pdb1.gz) 64 Kb
  • Biological Unit Coordinates (3iab.pdb2.gz) 125 Kb
  • LPC: Ligand-Protein Contacts for 3IAB
  • CSU: Contacts of Structural Units for 3IAB
  • Structure Factors (711 Kb)
  • Retrieve 3IAB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3IAB from S2C, [Save to disk]
  • Re-refined 3iab structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3IAB 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 3IAB
  • 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 3IAB, from MSDmotif at EBI
  • Fold representative 3iab from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3iab] [3iab_A] [3iab_R] [3iab_B]
  • SWISS-PROT database: [P53218] [P38291]
  • Domain organization of [POP6_YEAST] [POP7_YEAST] by SWISSPFAM
  • Other resources with information on 3IAB
  • Community annotation for 3IAB at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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