3HYC Hydrolase date Jun 22, 2009
title Crystal Structure Of E. Coli Phosphatase Yrbi, With Mg, Tetr Form
authors O.V.Tsodikov, T.Biswas
compound source
Molecule: 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Phosphat
Chain: A, B, C, D, E, F, G, H
Synonym: Kdo 8-P Phosphatase
Ec: 3.1.3.45
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 37762
Strain: B
Gene: Yrbi
symmetry Space Group: P 41 21 2
R_factor 0.242 R_Free 0.257
crystal
cell
length a length b length c angle alpha angle beta angle gamma
122.219 122.219 202.173 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.06 Å
ligand CL, MG enzyme Hydrolase E.C.3.1.3.45 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B, H, C, D, G
  • 3-deoxy-manno-octulosonate-8...


  • Primary referenceThe tail of KdsC: conformational changes control the activity of a haloacid dehalogenase superfamily phosphatase., Biswas T, Yi L, Aggarwal P, Wu J, Rubin JR, Stuckey JA, Woodard RW, Tsodikov OV, J Biol Chem. 2009 Oct 30;284(44):30594-603. Epub 2009 Sep 2. PMID:19726684
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (212 Kb) [Save to disk]
  • Biological Unit Coordinates (3hyc.pdb1.gz) 105 Kb
  • Biological Unit Coordinates (3hyc.pdb2.gz) 104 Kb
  • Biological Unit Coordinates (3hyc.pdb3.gz) 205 Kb
  • LPC: Ligand-Protein Contacts for 3HYC
  • CSU: Contacts of Structural Units for 3HYC
  • Structure Factors (333 Kb)
  • Retrieve 3HYC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3HYC from S2C, [Save to disk]
  • Re-refined 3hyc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3HYC 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 3HYC
  • 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 3HYC, from MSDmotif at EBI
  • Fold representative 3hyc from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3hyc_C] [3hyc_F] [3hyc_B] [3hyc_G] [3hyc_H] [3hyc_D] [3hyc] [3hyc_A] [3hyc_E]
  • SWISS-PROT database: [P67653]
  • Domain organization of [KDSC_ECOL6] by SWISSPFAM
  • Other resources with information on 3HYC
  • Community annotation for 3HYC 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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