3NPP - JenaLib

Title :   CRYSTAL STRUCTURE OF A PFAM DUF1093 FAMILY PROTEIN (BSU39620) FROM BACILLUS SUBTILIS AT 2.15 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   28 Jun 10 (Deposition) - 28 Jul 10 (Release) - 28 Jul 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A,B  (3x)

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 A Pfam Duf1093 Family Protein (Bsu39620) From Bacillus Subtilis At 2. 15 A Resolution
To Be Published
PubMed: search

Compounds

Molecule 1 - PFAM DUF1093 FAMILY PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	SPEEDET
	Expression System Strain	:	HK100
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	YXEA, BSU39620, HS74A
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	UNCHARACTERIZED PROTEIN YXEA

Structural Features

Chains, Units

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (3x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 18)

Asymmetric Unit (3, 18)

No.	Name	Count	Type	Full Name
1	GOL	7	Ligand/Ion	GLYCEROL
2	MSE	2	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	9	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 18)

No.	Name	Count	Type	Full Name
1	GOL	7	Ligand/Ion	GLYCEROL
2	MSE	2	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	9	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 54)

No.	Name	Count	Type	Full Name
1	GOL	21	Ligand/Ion	GLYCEROL
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	27	Ligand/Ion	SULFATE ION

Sites (16, 16)

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PRO A:33 , ILE A:35 , PHE A:74 , PHE A:75 , VAL A:95 , GLU A:96 , THR A:97 , TRP A:98 , HOH A:264 , PRO B:33	BINDING SITE FOR RESIDUE GOL A 203
02	AC2	SOFTWARE	LYS A:68 , HOH A:236 , HOH A:265 , GLY B:0	BINDING SITE FOR RESIDUE GOL A 204
03	AC3	SOFTWARE	LYS A:102 , GLU A:104 , SER A:109 , HOH A:223 , ASP B:108 , LYS B:115	BINDING SITE FOR RESIDUE GOL A 205
04	AC4	SOFTWARE	LYS A:78 , ARG A:81 , HOH A:237	BINDING SITE FOR RESIDUE GOL A 206
05	AC5	SOFTWARE	GLN A:43 , TYR A:85 , HOH A:262 , GOL B:202	BINDING SITE FOR RESIDUE GOL A 207
06	AC6	SOFTWARE	GLY A:0 , HOH A:315 , HOH B:308	BINDING SITE FOR RESIDUE SO4 A 208
07	AC7	SOFTWARE	HIS A:50 , SER A:52 , PRO A:53 , GLY A:54 , HOH A:322	BINDING SITE FOR RESIDUE SO4 A 209
08	AC8	SOFTWARE	GLN A:37 , LYS A:89 , SO4 A:211 , HOH A:235	BINDING SITE FOR RESIDUE SO4 A 210
09	AC9	SOFTWARE	LYS A:89 , LYS A:91 , SO4 A:210 , HOH A:231	BINDING SITE FOR RESIDUE SO4 A 211
10	BC1	SOFTWARE	ARG A:49 , GLU A:57 , HOH A:257 , LEU B:51 , SER B:52	BINDING SITE FOR RESIDUE SO4 A 213
11	BC2	SOFTWARE	PRO A:33 , GLN B:37 , PHE B:75 , LYS B:91 , GLU B:96 , TRP B:98 , HOH B:324	BINDING SITE FOR RESIDUE GOL B 201
12	BC3	SOFTWARE	TYR A:85 , GOL A:207 , TYR B:85	BINDING SITE FOR RESIDUE GOL B 202
13	BC4	SOFTWARE	PHE A:34 , HIS A:36 , HOH A:219 , HOH A:232 , LYS B:93 , TYR B:94 , HOH B:238 , HOH B:254	BINDING SITE FOR RESIDUE SO4 B 212
14	BC5	SOFTWARE	GLU A:71 , HOH A:301 , ARG B:30 , HIS B:50 , SER B:52 , PRO B:53 , GLY B:54	BINDING SITE FOR RESIDUE SO4 B 214
15	BC6	SOFTWARE	GLY B:0 , ARG B:30	BINDING SITE FOR RESIDUE SO4 B 215
16	BC7	SOFTWARE	ARG A:49 , HIS A:50 , SER A:52 , HOH A:299 , ARG B:49	BINDING SITE FOR RESIDUE SO4 B 216

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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:87
 aligned with YXEA_BACSU | P54940 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:87
                                    38        48        58        68        78        88        98       108       
           YXEA_BACSU    29 DRFNPFIHQQDVYVQIDRDGRHLSPGGTEYTLDGYNASGKKEEVTFFAGKELRKNAYLKVKAKGKYVETWEEVKFEDMPDSVQSKLK 115
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....eeeeeee.....eee...eeeeeeeee.....eeeeeeee........eeeeeee..eeeeeeeehhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 3npp A   0 GRFNPFIHQQDVYVQIDRDGRHLSPGGTEYTLDGYNASGKKEEVTFFAGKELRKNAYLKVKAKGKYVETWEEVKFEDmPDSVQSKLK 115
                            ||      38        48        58        68        78        88        98       108       
                            ||                                                                         106-MSE     
                            0|                                                                                     
                            30

Chain B from PDB  Type:PROTEIN  Length:87
 aligned with YXEA_BACSU | P54940 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:87
                                    38        48        58        68        78        88        98       108       
           YXEA_BACSU    29 DRFNPFIHQQDVYVQIDRDGRHLSPGGTEYTLDGYNASGKKEEVTFFAGKELRKNAYLKVKAKGKYVETWEEVKFEDMPDSVQSKLK 115
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....eeeeeee.....eee...eeeeeeeeee....eeeeeeee........eeeeeee..eeeeeeeehhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 3npp B   0 GRFNPFIHQQDVYVQIDRDGRHLSPGGTEYTLDGYNASGKKEEVTFFAGKELRKNAYLKVKAKGKYVETWEEVKFEDmPDSVQSKLK 115
                            ||      38        48        58        68        78        88        98       108       
                            0|                                                                         106-MSE     
                            30

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
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ 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 ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ser A:52 - Pro A:53	[ RasMol ]
		Ser B:52 - Pro B:53	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ 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 \| Biol. Unit 2 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
	3npp
		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
	YXEA_BACSU \| P54940
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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
	YXEA_BACSU \| P54940
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description