3SAF	Hydrolase	date	Jun 02, 2011
title	Crystal Structure Of The Human Rrp6 Catalytic Domain With D3 Mutation In The Active Site
authors	K.Januszyk, Q.Liu, C.D.Lima
compound		source
Molecule: Exosome Component 10 Chain: A, B Fragment: Unp Residues 180-606 Synonym: Rrp6, Autoantigen Pmscl 2, P100 Polymyositis-Scle Overlap Syndrome-Associated Autoantigen, Polymyositisscler Autoantigen 100 Kda, Pmscl-100, Polymyositisscleroderma A 2; Ec: 3.1.13.- Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Exosc10, Pmscl, Pmscl2, Rrp6 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Cp Ril Expression_system_vector_type: Plasmid Expression_system_plasmid: Psmt3 Sumo Fusion
symmetry	Space Group: P 4	R_factor 0.205 R_Free 0.240
crystal cell	length a length b length c angle alpha angle beta angle gamma 138.900 138.900 58.400 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.50 Å
ligand	MG, YT3	enzyme	Hydrolase E.C.3.1.13 BRENDA
Primary reference	Activities of human RRP6 and structure of the human RRP6 catalytic domain., Januszyk K, Liu Q, Lima CD, RNA. 2011 Jun 24. PMID:21705430

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (138 Kb) [Save to disk] Biological Unit Coordinates (3saf.pdb1.gz) 68 Kb Biological Unit Coordinates (3saf.pdb2.gz) 68 Kb LPC: Ligand-Protein Contacts for 3SAF CSU: Contacts of Structural Units for 3SAF Structure Factors (1475 Kb) Retrieve 3SAF in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3SAF from S2C, [Save to disk] Re-refined 3saf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3SAF 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 3SAF

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 3SAF, from MSDmotif at EBI Fold representative 3saf from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3saf_A] [3saf_B] SWISS-PROT database: Domain organization of by SWISSPFAM Alignments of the sequence of 3SAF with the sequences similar proteins can be viewed for 3SAF's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.

Other resources with information on 3SAF

Community annotation for 3SAF at PDBWiki (http://pdbwiki.org)

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