4X4F Gene Regulation date Dec 02, 2014
title Radiation Damage To The Nucleoprotein Complex C.Esp1396i: Do 20.6 Mgy
authors C.S.Bury, J.E.Mcgeehan, E.F.Garman
compound source
Molecule: Regulatory Protein
Chain: A, B, C, D
Fragment: Controller Protein
Engineered: Yes
Organism_scientific: Enterobacter Sp. Rfl1396
Organism_taxid: 211595
Gene: Esp1396ic
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Gold
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet23

Molecule: 35-Mer Dna
Chain: E
Fragment: Operator Dna
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Chemically Synthesised Dna

Molecule: 35-Mer Dna
Chain: F
Fragment: Operator Dna
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Chemically Synthesised Dna
symmetry Space Group: P 65
R_factor 0.237 R_Free 0.281
crystal
cell
length a length b length c angle alpha angle beta angle gamma
104.410 104.410 139.150 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.80 Å
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceRadiation damage to nucleoprotein complexes in macromolecular crystallography., Bury C, Garman EF, Ginn HM, Ravelli RB, Carmichael I, Kneale G, McGeehan JE, J Synchrotron Radiat. 2015 Mar;22(Pt 2):213-24. doi: 10.1107/S1600577514026289., Epub 2015 Jan 30. PMID:25723923
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (84 Kb) [Save to disk]
  • Biological Unit Coordinates (4x4f.pdb1.gz) 79 Kb
  • CSU: Contacts of Structural Units for 4X4F
  • Structure Factors (369 Kb)
  • Retrieve 4X4F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4X4F from S2C, [Save to disk]
  • Re-refined 4x4f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4X4F 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 4X4F
  • 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 4X4F, from MSDmotif at EBI
  • Fold representative 4x4f from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4x4f_E] [4x4f_C] [4x4f_D] [4x4f_B] [4x4f] [4x4f_A] [4x4f_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4X4F: [HTH_XRE ] by SMART
  • Other resources with information on 4X4F
  • Community annotation for 4X4F at PDBWiki (http://pdbwiki.org)

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