2RA9 - JenaLib

Title :   CRYSTAL STRUCTURE OF A DUF1285 FAMILY PROTEIN (SBAL_2486) FROM SHEWANELLA BALTICA OS155 AT 1.40 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   14 Sep 07 (Deposition) - 16 Oct 07 (Release) - 24 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

Chains :   Asym./Biol. Unit : A

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

Reference :   G. W. Han, C. Bakolitsa, M. D. Miller, A. Kumar, D. Carlton, R. J. Najmanovich, P. Abdubek, T. Astakhova, H. L. Axelrod, C. Chen, H. J. Chiu, T. Clayton, D. Das, M. C. Deller, L. Duan, D. Ernst, J. Feuerhelm, J. C. Grant, A. Grzechnik, L. Jaroszewski, K. K. Jin, H. A. Johnson, H. E. Klock, M. W. Knuth, P. Kozbial, S. S. Krishna, D. Marciano, D. Mcmullan, A. T. Morse, E. Nigoghossian, L. Okach, R. Reyes, C. L. Rife, N. Sefcovic, H. J. Tien, C. B. Trame, H. Van Den Bedem, D. Weekes, Q. Xu, K. O. Hodgson, J. Wooley, M. A. Elsliger, A. M. Deacon, A. Godzik, S. A. Lesley, I. A. Wilson
Structures Of The First Representatives Of Pfam Family Pf06938 (Duf1285) Reveal A New Fold With Repeated Structura Motifs And Possible Involvement In Signal Transduction.
Acta Crystallogr. , Sect. F V. 66 1218 2010
PubMed-ID: 20944214 | Reference-DOI: 10.1107/S1744309109050416

Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN DUF1285
	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
	Fragment	:	RESIDUES 9-157
	Gene	:	YP_001050848.1, SBAL_2486
	Organism Scientific	:	SHEWANELLA BALTICA
	Organism Taxid	:	325240
	Strain	:	OS155

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:147 , PHE A:149 , HOH A:167 , HOH A:195 , HOH A:264 , HOH A:266	BINDING SITE FOR RESIDUE NA A 158
2	AC2	SOFTWARE	ASP A:35 , PRO A:73 , VAL A:74 , GLU A:75 , LYS A:76 , HOH A:196 , HOH A:344	BINDING SITE FOR RESIDUE EDO A 159
3	AC3	SOFTWARE	ASP A:90 , CYS A:141 , ASN A:144	BINDING SITE FOR RESIDUE EDO A 160
4	AC4	SOFTWARE	GLY A:138 , ARG A:139 , HOH A:175 , HOH A:209	BINDING SITE FOR RESIDUE EDO A 161
5	AC5	SOFTWARE	ASP A:123 , SER A:124 , VAL A:125 , LEU A:137 , ARG A:139 , TYR A:142 , HOH A:307	BINDING SITE FOR RESIDUE EDO A 162
6	AC6	SOFTWARE	SER A:103 , GLY A:107 , ASP A:122	BINDING SITE FOR RESIDUE EDO A 163
7	AC7	SOFTWARE	GLU A:75 , ASN A:147 , HOH A:167 , HOH A:229	BINDING SITE FOR RESIDUE EDO A 164
8	AC8	SOFTWARE	SER A:29 , ARG A:139 , TYR A:142 , TYR A:143 , HOH A:378 , HOH A:386	BINDING SITE FOR RESIDUE EDO A 165

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/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:127
 aligned with A3D5G6_SHEB5 | A3D5G6 from UniProtKB/TrEMBL  Length:157

    Alignment length:127
                                    38        48        58        68        78        88        98       108       118       128       138       148       
         A3D5G6_SHEB5    29 SEVPLFDINALGDWTYLGTSLPAKFAKLFASILHCIDDEYFLITPVEKVRVQVEDAPLLIVDFERAQPHSLLNVSTSIGTLHHNVDIKQMKLTDDSVYLPLERGLWGKLGRACYYNFVNEFNLSDLN 155
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ra9A01 A:29-82 duf1285 like domain                   2ra9A02 A:83-155 duf1285 protein                                          CATH domains
               Pfam domains -----DUF1285-2ra9A01 A:34-155                                                                                                   Pfam domains
         Sec.struct. author .....eee.....eee..ee.hhhhhhhhhh.eeee..eeeee....eeeeee....eeeeeeee......eeeee....eeeeehhhhhee....eeee.....eeee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ra9 A  29 SEVPLFDINALGDWTYLGTSLPAKFAKLFASILHCIDDEYFLITPVEKVRVQVEDAPLLIVDFERAQPHSLLNVSTSIGTLHHNVDIKQmKLTDDSVYLPLERGLWGKLGRACYYNFVNEFNLSDLN 155
                                    38        48        58        68        78        88        98       108       118       128       138       148       
                                                                                                                   118-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 (2, 2)

Pfam Domains (1, 1)

Gene Ontology (0, 0)

Visualization

Interactive Views

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
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ 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 2ra9)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2ra9
		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
	A3D5G6_SHEB5 \| A3D5G6
		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
	A3D5G6_SHEB5 \| A3D5G6
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description