3F7X - JenaLib

Title :   CRYSTAL STRUCTURE OF A PUTATIVE POLYKETIDE CYCLASE (PP0894) FROM PSEUDOMONAS PUTIDA KT2440 AT 1.24 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   10 Nov 08 (Deposition) - 25 Nov 08 (Release) - 23 Mar 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.24

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Polyketide Cyclase. (Np_743055. 1) From Pseudomonas Putida Kt2440 At 1. 24 A Resolution
To Be Published
PubMed: search

Compounds

Molecule 1 - PUTATIVE POLYKETIDE CYCLASE
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	SPEEDET
	Expression System Strain	:	HK100
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NP_743055.1, PP0894, PP_0894
	Organism Scientific	:	PSEUDOMONAS PUTIDA KT2440
	Organism Taxid	:	160488

Structural Features

Chains, Units

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 14)

Asymmetric Unit (3, 14)

No.	Name	Count	Type	Full Name
1	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
3	UNL	2	Ligand/Ion	UNKNOWN LIGAND

Biological Unit 1 (3, 28)

No.	Name	Count	Type	Full Name
1	EDO	12	Ligand/Ion	1,2-ETHANEDIOL
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
3	UNL	4	Ligand/Ion	UNKNOWN LIGAND

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MSE A:53 , TYR A:57 , GLU A:59 , ALA A:104 , ASN A:120 , TYR A:122 , TRP A:127 , UNL A:134 , EDO A:135 , HOH A:195 , HOH A:201 , HOH A:239 , HOH A:249	BINDING SITE FOR RESIDUE UNL A 133
2	AC2	SOFTWARE	PHE A:49 , MSE A:53 , ASP A:89 , UNL A:133 , HOH A:146 , HOH A:158 , HOH A:268 , HOH A:275	BINDING SITE FOR RESIDUE UNL A 134
3	AC3	SOFTWARE	TYR A:10 , HIS A:32 , ASN A:120 , UNL A:133 , HOH A:196	BINDING SITE FOR RESIDUE EDO A 135
4	AC4	SOFTWARE	PHE A:14 , GLY A:17 , MSE A:53 , ASN A:54 , ARG A:58 , GLU A:59 , HOH A:160 , HOH A:199 , HOH A:280	BINDING SITE FOR RESIDUE EDO A 136
5	AC5	SOFTWARE	ARG A:74 , TYR A:109 , ARG A:117 , EDO A:140 , HOH A:279	BINDING SITE FOR RESIDUE EDO A 137
6	AC6	SOFTWARE	ARG A:58 , ARG A:60 , HIS A:82 , HOH A:177 , HOH A:187 , HOH A:300 , HOH A:314	BINDING SITE FOR RESIDUE EDO A 138
7	AC7	SOFTWARE	ASP A:71 , GLY A:72 , SER A:73 , ILE A:110 , CYS A:112 , GLY A:113 , HOH A:216 , HOH A:237 , HOH A:238 , HOH A:252	BINDING SITE FOR RESIDUE EDO A 139
8	AC8	SOFTWARE	PHE A:79 , THR A:80 , EDO A:137 , HOH A:188	BINDING SITE FOR RESIDUE EDO A 140

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

Asymmetric 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:133
 aligned with Q88PF6_PSEPK | Q88PF6 from UniProtKB/TrEMBL  Length:132

    Alignment length:133
                             1                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129   
         Q88PF6_PSEPK     - -MTATELVNAYYAAFNAGDMPAFLALLSEDVIHDINQGERQMGKARFAAFMEKMNRCYRERLADIVVMQNADGSRAAAEFTVHGQYLADDEGLPTANGQTYVLPAGAFFYIHCGKIARVTNYYNLNDWVEQVA 132
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhheeeeeeee.....eeehhhhhhhhhhhhhhheeeeeeeeeeee.....eeeeeeeeeeee.............eeeeeeeeeeeee..eeeeeeeeehhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f7x A   0 GmTATELVNAYYAAFNAGDmPAFLALLSEDVIHDINQGERQmGKARFAAFmEKmNRCYRERLADIVVmQNADGSRAAAEFTVHGQYLADDEGLPTANGQTYVLPAGAFFYIHCGKIARVTNYYNLNDWVEQVA 132
                             |       9        19        29        39 |      49|  |    59       |69        79        89        99       109       119       129   
                             |                19-MSE                41-MSE   50-MSE           67-MSE                                                             
                             1-MSE                                              53-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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

Visualization

Interactive Views

Asymmetric 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
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		UNL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3f7x)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - 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)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3f7x
		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
	Q88PF6_PSEPK \| Q88PF6
		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

Analysis Tools

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
	Q88PF6_PSEPK \| Q88PF6
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description