3UWA - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A PROBABLE PEPTIDE DEFORMYLASE FROM SYNECHOCOCCUS PHAGE S-SSM7

Authors :   D. Lorimer, J. Abendroth, T. E. Edwards, A. Burgin, A. Segall, F. Rohwer

Date :   01 Dec 11 (Deposition) - 09 Jan 13 (Release) - 19 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym./Biol. Unit : A

Keywords :   Synechococcus Phage, Probable Peptide Deformylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. A. Frank, D. Lorimer, M. Youle, P. Witte, T. Craig, J. Abendroth, F. Rohwer, R. A. Edwards, A. M. Segall, A. B. Burgin
Structure And Function Of A Cyanophage-Encoded Peptide Deformylase.
Isme J V. 7 1150 2013
PubMed-ID: 23407310 | Reference-DOI: 10.1038/ISMEJ.2013.4

Molecule 1 - RIIA-RIIB MEMBRANE-ASSOCIATED PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	VCID 5538
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SSSM7_299, YP_004324347.1
	Organism Scientific	:	SYNECHOCOCCUS PHAGE S-SSM7
	Organism Taxid	:	445686
	Strain	:	8109-3

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 7)

No.	Name	Count	Type	Full Name
1	MRD	2	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
3	ZN	1	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:92 , HIS A:134 , HIS A:138 , HOH A:221	BINDING SITE FOR RESIDUE ZN A 200
2	AC2	SOFTWARE	GLU A:61 , HIS A:71 , LEU A:124 , HOH A:264	BINDING SITE FOR RESIDUE MRD A 201
3	AC3	SOFTWARE	ASP A:60 , GLU A:61 , ALA A:128 , HOH A:162 , HOH A:230 , HOH A:236 , HOH A:264	BINDING SITE FOR RESIDUE MRD A 202

(no "SS Bond" information available for 3UWA)

(no "Cis Peptide Bond" information available for 3UWA)

(no "SAP(SNP)/Variant" information available for 3UWA)

(no "PROSITE Motif" information available for 3UWA)

(no "Exon" information available for 3UWA)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:148
 aligned with E3SLL2_9CAUD | E3SLL2 from UniProtKB/TrEMBL  Length:128

    Alignment length:148
                                                     1                                                                                                                          
                                     -         -     |   5        15        25        35        45        55        65        75        85        95       105       115        
         E3SLL2_9CAUD     - -------------------------MSELYDQMCEAMWASDGIGLAAPQVGINKRVIVVDETTEEHGKYAHLMVNPKITWKSEEKVLFDEGCLSVPDQNGEVLRPKSIKVTFQNKDGKYKKWKLDGLAARVVQHEIDHLEGILFVDYF 123
               SCOP domains d3uwaa_ A: automated matches                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh........hhhhhhhhhhhhhhhhhhh...eee.hhhh....eeeee.........eeeeeeeeeeee...eeeeee.........eeeeee..eeeeee.....eeeeeehhhhhhhhhhhhhhhh..hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uwa A   1 SLKIKTIGDRCLRQKSEEVEFDKKEmSELYDQmCEAmWASDGIGLAAPQVGINKRVIVVDETTEEHGKYAHLmVNPKITWKSEEKVLFDEGCLSVPDQNGEVLRPKSIKVTFQNKDGKYKKWKLDGLAARVVQHEIDHLEGILFVDYF 148
                                    10        20     |  30  |   | 40        50        60        70  |     80        90       100       110       120       130       140        
                                                    26-MSE 33-MSE                                  73-MSE                                                                       
                                                               37-MSE

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Peptide deformylase (87)

Superfamily: Peptide deformylase (87)

Family: automated matches (25)

Protein domain: automated matches (25)

Synechococcus phage [TaxId: 445686] (2)

d3uwaa_

(no "CATH Domain" information available for 3UWA)

(no "Pfam Domain" information available for 3UWA)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (E3SLL2_9CAUD | E3SLL2)


GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
GO:0042586	peptide deformylase activity	Catalysis of the reaction: formyl-L-methionyl peptide + H2O = formate + methionyl peptide.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		MRD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3uwa)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3uwa
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	E3SLL2_9CAUD \| E3SLL2
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	E3SLL2_9CAUD \| E3SLL2
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	E3SLL2_9CAUD \| E3SLL2	:	3uwb

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (3, 3)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File