2HVY Isomerase Biosynthetic Protein Rna date Jul 31, 2006
title Crystal Structure Of An Haca Box Rnp From Pyrococcus Furios
authors K.Ye
compound source
Molecule: Haca Rna
Chain: E
Engineered: Yes
Synthetic: Yes
Other_details: Derived From Afu-46 Rna

Molecule: Probable Trna Pseudouridine Synthase B
Chain: A
Synonym: Trna Pseudouridine 55 Synthase, Psi55 Synthase, Tr Isomerase, Trna Pseudouridylate Synthase;
Ec: 5.4.99.-
Engineered: Yes

Organism_scientific: Pyrococcus Furiosus
Organism_taxid: 2261
Gene: Trub
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Rosseta2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Petduet-1

Molecule: Small Nucleolar Rnp Similar To Gar1
Chain: B
Synonym: Gar1
Engineered: Yes

Organism_scientific: Pyrococcus Furiosus
Organism_taxid: 2261
Gene: Gar1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Rosseta2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prsfduet-1

Molecule: Ribosome Biogenesis Protein Nop10
Chain: C
Synonym: Nop10
Engineered: Yes
Mutation: Yes

Organism_scientific: Pyrococcus Furiosus
Organism_taxid: 2261
Gene: Nop10
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Rosseta2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Petduet-1

Molecule: 50s Ribosomal Protein L7ae
Chain: D
Synonym: L7ae
Engineered: Yes
Mutation: Yes

Organism_scientific: Pyrococcus Furiosus
Organism_taxid: 2261
Gene: Rpl7ae
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Rosseta2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prsfduet-1
symmetry Space Group: P 21 21 21
R_factor 0.238 R_Free 0.278
crystal
cell
length a length b length c angle alpha angle beta angle gamma
83.031 90.950 114.064 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand ATP, ZN enzyme Isomerase E.C.5.4.99 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


D
  • ribonuclease P activity


  • Primary referenceCrystal structure of an H/ACA box ribonucleoprotein particle., Li L, Ye K, Nature. 2006 Aug 30;. PMID:16943774
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (124 Kb) [Save to disk]
  • Biological Unit Coordinates (2hvy.pdb1.gz) 116 Kb
  • LPC: Ligand-Protein Contacts for 2HVY
  • CSU: Contacts of Structural Units for 2HVY
  • Likely Quarternary Molecular Structure file(s) for 2HVY
  • Structure Factors (285 Kb)
  • Retrieve 2HVY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2HVY from S2C, [Save to disk]
  • Re-refined 2hvy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2HVY 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 2HVY
  • 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 2HVY, from MSDmotif at EBI
  • Fold representative 2hvy from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2hvy_B] [2hvy_A] [2hvy_D] [2hvy] [2hvy_E] [2hvy_C]
  • SWISS-PROT database: [Q8U1R4] [Q8U029] [Q8U160] [Q7LWY0]
  • Domain organization of [NOP10_PYRFU] [Q8U029_PYRFU] [RL7A_PYRFU] [TRUB_PYRFU] by SWISSPFAM
  • Domains found in 2HVY: [DKCLD] [PUA ] by SMART
  • Other resources with information on 2HVY
  • Community annotation for 2HVY at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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