3E54	Hydrolase Dna	date	Aug 13, 2008
title	Archaeal Intron-Encoded Homing Endonuclease I-Vdi141i Comple Dna
authors	N.Nomura, Y.Nomura, D.Sussman, B.L.Stoddard
compound		source
Molecule: Rrna Intron-Encoded Endonuclease Chain: A, B Synonym: Homing Endonuclease I-Vdi141i Ec: 3.1.-.- Engineered: Yes Mutation: Yes		Organism_scientific: Vulcanisaeta Distributa Organism_taxid: 164451 Strain: Ic-141 Gene: 23s Rrna Intron (Vdi141.L1927) Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21-Codonplus (De3)-Ril Expression_system_vector_type: Plasmid Expression_system_plasmid: Pvdii65mi107m-10
Molecule: Dna (5'- D(Dcpdtpdgpdapdcpdtpdcpdtpdcpdtpdtpdapda)-3'); Chain: C Engineered: Yes Other_details: I-Vdi141i Dna Target Site		Synthetic: Yes
Molecule: Dna (5'-D(Pdgpdgpdtpdapdgpdcpdcpdapda)-3 Chain: D Engineered: Yes Other_details: I-Vdi141i Dna Target Site		Synthetic: Yes
Molecule: Dna (5'- D(Dtpdtpdgpdgpdcpdtpdapdcpdcpdtpdtpdapda)-3'); Chain: E Engineered: Yes Other_details: I-Vdi141i Dna Target Site		Synthetic: Yes
Molecule: Dna (5'-D(Pdgpdapdgpdapdgpdtpdcpdapdg)-3 Chain: F Engineered: Yes Other_details: I-Vdi141i Dna Target Site		Synthetic: Yes
symmetry	Space Group: P 61	R_factor 0.231 R_Free 0.250
crystal cell	length a length b length c angle alpha angle beta angle gamma 66.580 66.580 217.910 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.50 Å
ligand	EOH, MG	enzyme	Hydrolase E.C.3.1 BRENDA
Gene Ontology	Chain Function Process Component A, B endonuclease activity
Primary reference	Recognition of a common rDNA target site in archaea and eukarya by analogous LAGLIDADG and His-Cys box homing endonucleases., Nomura N, Nomura Y, Sussman D, Klein D, Stoddard BL, Nucleic Acids Res. 2008 Dec;36(22):6988-98. Epub 2008 Nov 4. PMID:18984620

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk] Biological Unit Coordinates (3e54.pdb1.gz) 73 Kb LPC: Ligand-Protein Contacts for 3E54 CSU: Contacts of Structural Units for 3E54 Likely Quarternary Molecular Structure file(s) for 3E54 Structure Factors (229 Kb) Retrieve 3E54 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3E54 from S2C, [Save to disk] Re-refined 3e54 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3E54 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 3E54

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 3D motif for 3E54, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3e54] [3e54_D] [3e54_F] [3e54_B] [3e54_E] [3e54_A] [3e54_C] SWISS-PROT database: [Q6L703] Domain organization of [Q6L703_9CREN] by SWISSPFAM

Other resources with information on 3E54

Community annotation for 3E54 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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