3MX4 Hydrolase Dna date May 06, 2010
title Dna Binding And Cleavage By The Giy-Yig Endonuclease R.Eco29 Inactive Variant E142q
authors A.N.S.Mak, A.R.Lambert, B.L.Stoddard
compound source
Molecule: Eco29kir
Chain: A, B, C, D, E, F, G, H
Synonym: Restriction Endonuclease
Ec: 3.1.21.4
Engineered: Yes
Mutation: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Eco29kir
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-15he

Molecule: Dna (5'- D(Pcpgpgpgpapgpgpcpcpcpgpcpgpgpgpcpcpgpc -3');
Chain: I, K, M, O
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'- D(Pgpcpgpgpcpgpgpcpcpcpgpcpgpgpgpcpcptpc -3');
Chain: J, L, N, P
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.211 R_Free 0.274
crystal
cell
length a length b length c angle alpha angle beta angle gamma
99.855 101.463 144.403 90.00 110.19 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand
enzyme Hydrolase E.C.3.1.21.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B, H, C, D, G


Primary referenceFolding, DNA Recognition, and Function of GIY-YIG Endonucleases: Crystal Structures of R.Eco29kI., Mak AN, Lambert AR, Stoddard BL, Structure. 2010 Aug 25. PMID:20800503
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (732 Kb) [Save to disk]
  • Biological Unit Coordinates (3mx4.pdb1.gz) 184 Kb
  • Biological Unit Coordinates (3mx4.pdb2.gz) 183 Kb
  • Biological Unit Coordinates (3mx4.pdb3.gz) 183 Kb
  • Biological Unit Coordinates (3mx4.pdb4.gz) 181 Kb
  • CSU: Contacts of Structural Units for 3MX4
  • Structure Factors (2485 Kb)
  • Retrieve 3MX4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3MX4 from S2C, [Save to disk]
  • Re-refined 3mx4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3MX4 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 3MX4
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3MX4, from MSDmotif at EBI
  • Fold representative 3mx4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3mx4_F] [3mx4_K] [3mx4_I] [3mx4_C] [3mx4_A] [3mx4_D] [3mx4] [3mx4_L] [3mx4_M] [3mx4_P] [3mx4_B] [3mx4_E] [3mx4_N] [3mx4_G] [3mx4_H] [3mx4_J] [3mx4_O]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3MX4
  • Community annotation for 3MX4 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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