1JVA	Hydrolase	date	Aug 29, 2001
title	Crystal Structure Of The Vma1-Derived Endonuclease Bearing T Extein Propeptides
authors	R.Mizutani, Y.Satow
compound		source
Molecule: Vma1-Derived Homing Endonuclease X10sss Chain: A, B Fragment: Residues 274-747 Synonym: X10sss Vde Ec: 3.6.1.34 Engineered: Yes Mutation: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Gene: Vma1 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet-17b-Vde-X10sss
symmetry	Space Group: P 1	R_factor 0.198 R_Free 0.240
crystal cell	length a length b length c angle alpha angle beta angle gamma 66.178 68.846 58.524 103.10 98.79 78.98
method	X-Ray Diffraction	resolution	2.10 Å
ligand		enzyme	Hydrolase E.C.3.6.1.34 BRENDA
note	1JVA (Molecule of the Month:pdb131)
related structures	by homologous chain: 1DFA, 1EF0
Gene Ontology	Chain Function Process Component A, B
Primary reference	Protein-splicing reaction via a thiazolidine intermediate: crystal structure of the VMA1-derived endonuclease bearing the N and C-terminal propeptides., Mizutani R, Nogami S, Kawasaki M, Ohya Y, Anraku Y, Satow Y, J Mol Biol 2002 Mar 1;316(4):919-29. PMID:11884132

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (143 Kb) [Save to disk] Biological Unit Coordinates (1jva.pdb1.gz) 70 Kb Biological Unit Coordinates (1jva.pdb2.gz) 71 Kb CSU: Contacts of Structural Units for 1JVA Likely Quarternary Molecular Structure file(s) for 1JVA Retrieve 1JVA in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1JVA from S2C, [Save to disk]

View 1JVA 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 1JVA

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1JVA, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1jvaa1, region A:282-463,A:699-741 [Jmol] [rasmolscript] [script source]     - Domain d1jvaa2, region A:464-581 [Jmol] [rasmolscript] [script source]     - Domain d1jvaa3, region A:582-698 [Jmol] [rasmolscript] [script source]     - Domain d1jvab1, region B:279-463,B:699-741 [Jmol] [rasmolscript] [script source]     - Domain d1jvab2, region B:464-581 [Jmol] [rasmolscript] [script source]     - Domain d1jvab3, region B:582-698 [Jmol] [rasmolscript] [script source] Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1jva] [1jva_B] [1jva_A] SWISS-PROT database: [P17255] Belongs to the h(+)- or na(+)-translocating f-type, v-type and a-type atpase (f-atpase) superfamily according to TCDB. Domain organization of [VATA_YEAST] by SWISSPFAM Domains found in 1JVA: [HintC] [HintN ] by SMART

Other resources with information on 1JVA

Community annotation for 1JVA at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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