4ERN Hydrolase date Apr 20, 2012
title Crystal Structure Of The C-Terminal Domain Of Human Xpbercc Excision Repair Protein At 1.80 A
authors E.Hilario, Y.Li, L.Fan
compound source
Molecule: Tfiih Basal Transcription Factor Complex Helicase Subunit;
Chain: A
Fragment: C-Terminal Domain (Unp Residues 494-782)
Synonym: Basic Transcription Factor 2 89 Kda Subunit, Btf2 Excision Repair Protein Ercc-3, Dna Repair Protein Compleme Cells, Tfiih Basal Transcription Factor Complex 89 Kda Subu 89 Kda Subunit, Tfiih P89, Xeroderma Pigmentosum Group B- Complementing Protein;
Ec: 3.6.4.12
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ercc3, Xpb, Xpbc
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta(De3)Plys-S
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex6p1
symmetry Space Group: P 21 21 21
R_factor 0.201 R_Free 0.238
crystal
cell
length a length b length c angle alpha angle beta angle gamma
38.260 73.650 84.300 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand
enzyme Hydrolase E.C.3.6.4.12 BRENDA
Primary referenceStructure of the C-terminal half of human XPB helicase and the impact of the disease-causing mutation XP11BE., Hilario E, Li Y, Nobumori Y, Liu X, Fan L, Acta Crystallogr D Biol Crystallogr. 2013 Feb;69(Pt 2):237-46. doi:, 10.1107/S0907444912045040. Epub 2013 Jan 19. PMID:23385459
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (88 Kb) [Save to disk]
  • Biological Unit Coordinates (4ern.pdb1.gz) 82 Kb
  • CSU: Contacts of Structural Units for 4ERN
  • Structure Factors (154 Kb)
  • Retrieve 4ERN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4ERN from S2C, [Save to disk]
  • Re-refined 4ern structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4ERN 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 4ERN
  • 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 4ERN, from MSDmotif at EBI
  • Fold representative 4ern from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ern] [4ern_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4ERN: [HELICc ] by SMART
  • Alignments of the sequence of 4ERN with the sequences similar proteins can be viewed for 4ERN's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 4ERN
  • Community annotation for 4ERN at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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