3R7P Hydrolase Dna date Mar 22, 2011
title The Crystal Structure Of I-Ltri
authors A.N.S.Mak, R.Takeuchi, D.R.Edgell, B.L.Stoddard
compound source
Molecule: Ribosomal Protein 3homing Endonuclease-Like Fusi Protein;
Chain: A
Fragment: I-Ltri (Unp Residues 398-712)
Engineered: Yes
Organism_scientific: Leptographium Truncatum
Organism_taxid: 330483
Gene: Rps3heg Fusion
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Ril (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-200-D-Topo

Molecule: Dna (5'-D(Gpgptpcptpapapapcpgptpcpgp 3');
Chain: B
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic

Molecule: Dna (5'-D(Papgpgpapgpcpaptptptpg)-3')
Chain: C
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic

Molecule: Dna (5'-D(Cpapapaptpgpcptpcpcptpaptp 3');
Chain: D
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic

Molecule: Dna (5'-D(Pgpapcpgptptptpapgpapcpc)-3
Chain: E
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic
symmetry Space Group: C 1 2 1
R_factor 0.192 R_Free 0.270
length a length b length c angle alpha angle beta angle gamma
113.089 42.595 103.195 90.00 110.63 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand MG, MN enzyme Hydrolase E.C. BRENDA

Primary referenceTapping natural reservoirs of homing endonucleases for targeted gene modification., Takeuchi R, Lambert AR, Mak AN, Jacoby K, Dickson RJ, Gloor GB, Scharenberg AM, Edgell DR, Stoddard BL, Proc Natl Acad Sci U S A. 2011 Jul 22. PMID:21784983
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (149 Kb) [Save to disk]
  • Biological Unit Coordinates (3r7p.pdb1.gz) 143 Kb
  • LPC: Ligand-Protein Contacts for 3R7P
  • CSU: Contacts of Structural Units for 3R7P
  • Structure Factors (248 Kb)
  • Retrieve 3R7P in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3R7P from S2C, [Save to disk]
  • Re-refined 3r7p structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3R7P 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 3R7P
  • 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 3R7P, from MSDmotif at EBI
  • Fold representative 3r7p from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3r7p_E] [3r7p_D] [3r7p_A] [3r7p_C] [3r7p] [3r7p_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3R7P
  • Community annotation for 3R7P at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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