4B5G Hydrolase Dna date Aug 03, 2012
title Substrate Bound Neisseria Ap Endonuclease In Absence Of Meta (Crystal Form 2)
authors D.Lu, J.Silhan, J.T.Macdonald, E.P.Carpenter, K.Jensen, C.M.Tang, G.S.Baldwin, P.S.Freemont
compound source
Molecule: Exodeoxyribonuclease
Chain: A, B, C
Synonym: Neisseria Ap Endonuclease
Ec: 3.1.11.2
Engineered: Yes
Organism_scientific: Neisseria Meningitidis
Organism_taxid: 487
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: 5'-D(Gpcptpapcp(3dr)Pcpaptpcpgp)-3'
Chain: U, W, Y
Synonym: Dna 11mer Containing Abasic Residue
Engineered: Yes

Synthetic: Yes
Organism_scientific: Neisseria Meningitidis
Organism_taxid: 487

Molecule: 5'-D(Cpgpaptpgpgpgptpapgpcp)-3'
Chain: V, X, Z
Engineered: Yes

Synthetic: Yes
Organism_scientific: Neisseria Meningitidis
Organism_taxid: 487
symmetry Space Group: P 41 21 2
R_factor 0.232 R_Free 0.259
crystal
cell
length a length b length c angle alpha angle beta angle gamma
75.241 75.241 380.683 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.75 Å
ligand 3DR enzyme Hydrolase E.C.3.1.11.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C, B
  • nuclease activity
  • endonuclease activity
  • phosphodiesterase I activity...
  • double-stranded DNA 3'-5' ex...


  • Primary referenceStructural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis., Lu D, Silhan J, Macdonald JT, Carpenter EP, Jensen K, Tang CM, Baldwin GS, Freemont PS, Proc Natl Acad Sci U S A. 2012 Oct 3. PMID:23035246
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (159 Kb) [Save to disk]
  • Biological Unit Coordinates (4b5g.pdb1.gz) 53 Kb
  • Biological Unit Coordinates (4b5g.pdb2.gz) 53 Kb
  • Biological Unit Coordinates (4b5g.pdb3.gz) 53 Kb
  • LPC: Ligand-Protein Contacts for 4B5G
  • CSU: Contacts of Structural Units for 4B5G
  • Structure Factors (202 Kb)
  • Retrieve 4B5G in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4B5G from S2C, [Save to disk]
  • Re-refined 4b5g structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4B5G 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 4B5G
  • 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 4B5G, from MSDmotif at EBI
  • Fold representative 4b5g from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4b5g_V] [4b5g_A] [4b5g_X] [4b5g_B] [4b5g_U] [4b5g_C] [4b5g_Y] [4b5g] [4b5g_W] [4b5g_Z]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4B5G
  • Community annotation for 4B5G at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
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