1XAF - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF PROTEIN OF UNKNOWN FUNCTION YFIH FROM SHIGELLA FLEXNERI 2A STR. 2457T

Authors :   Y. Kim, N. Maltseva, I. Dementieva, F. Collart, A. Joachimiak, Midwest For Structural Genomics (Mcsg)

Date :   25 Aug 04 (Deposition) - 31 Aug 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.01

Chains :   Asym./Biol. Unit : A,B

Keywords :   Structural Genomics, Protein Structure Initiative, Mcsg, Hypothetical Protein, Yfih, Shigella Flexneri 2A Str. 2457T, Psi, Midwest Center For Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Kim, N. Maltseva, I. Dementieva, F. Collart, D. Holzle, A. Joachimiak
Crystal Structure Of Hypothetical Protein Yfih From Shigell Flexneri At 2 A Resolution.
Proteins V. 63 1097 2006
PubMed-ID: 16498617 | Reference-DOI: 10.1002/PROT.20589

Molecule 1 - ORF, CONSERVED HYPOTHETICAL PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	YFIH
	Organism Scientific	:	SHIGELLA FLEXNERI 2A
	Organism Taxid	:	198215
	Strain	:	2457T

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 21)

No.	Name	Count	Type	Full Name
1	ACT	5	Ligand/Ion	ACETATE ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
4	ZN	8	Ligand/Ion	ZINC ION

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:71 , CYS A:107 , HIS A:124 , ACT A:512	BINDING SITE FOR RESIDUE ZN A 501
02	AC2	SOFTWARE	HIS A:46 , GLU A:147 , GLU A:208 , HOH A:640	BINDING SITE FOR RESIDUE ZN A 502
03	AC3	SOFTWARE	CYS A:216 , THR A:219 , ACT A:514 , HOH A:538	BINDING SITE FOR RESIDUE ZN A 503
04	AC4	SOFTWARE	HIS A:186 , HOH A:646 , HIS B:39 , HOH B:666	BINDING SITE FOR RESIDUE ZN A 504
05	AC5	SOFTWARE	HIS B:71 , CYS B:107 , HIS B:124 , ACT B:513	BINDING SITE FOR RESIDUE ZN B 505
06	AC6	SOFTWARE	HIS B:46 , GLU B:208	BINDING SITE FOR RESIDUE ZN B 506
07	AC7	SOFTWARE	CYS B:216 , THR B:219 , ACT B:515 , ACT B:516	BINDING SITE FOR RESIDUE ZN B 507
08	AC8	SOFTWARE	HIS A:39 , HIS B:186 , HOH B:562 , HOH B:657	BINDING SITE FOR RESIDUE ZN A 508
09	AC9	SOFTWARE	HIS A:71 , THR A:104 , ALA A:105 , ASP A:106 , CYS A:107 , HIS A:124 , ARG A:235 , ZN A:501	BINDING SITE FOR RESIDUE ACT A 512
10	BC1	SOFTWARE	HIS B:71 , THR B:104 , ALA B:105 , CYS B:107 , HIS B:124 , ZN B:505	BINDING SITE FOR RESIDUE ACT B 513
11	BC2	SOFTWARE	GLY A:158 , PRO A:159 , ARG A:160 , CYS A:216 , THR A:219 , ZN A:503 , HOH A:541	BINDING SITE FOR RESIDUE ACT A 514
12	BC3	SOFTWARE	HIS A:39 , ARG B:160 , ALA B:161 , THR B:219 , ZN B:507 , ACT B:516	BINDING SITE FOR RESIDUE ACT B 515
13	BC4	SOFTWARE	GLY B:158 , PRO B:159 , ARG B:160 , CYS B:216 , THR B:219 , ZN B:507 , ACT B:515	BINDING SITE FOR RESIDUE ACT B 516
14	BC5	SOFTWARE	GLY A:37 , ALA A:38 , HIS A:39 , ARG A:51 , MSE A:103	BINDING SITE FOR RESIDUE GOL A 510
15	BC6	SOFTWARE	GLY B:37 , ALA B:38 , HIS B:39 , ARG B:51 , MSE B:103 , HOH B:649 , HOH B:653 , HOH B:708	BINDING SITE FOR RESIDUE GOL B 511

(no "SS Bond" information available for 1XAF)

Asymmetric/Biological Unit

No.	Residues
1	Pro A:29	-	Pro A:30
2	Asp A:32	-	Ser A:33
3	Pro B:29	-	Pro B:30
4	Asp B:32	-	Ser B:33

(no "SAP(SNP)/Variant" information available for 1XAF)

(no "PROSITE Motif" information available for 1XAF)

(no "Exon" information available for 1XAF)

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:242
 aligned with Q83K13_SHIFL | Q83K13 from UniProtKB/TrEMBL  Length:243

    Alignment length:242
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241  
         Q83K13_SHIFL     2 SKLIVPQWPLPKGVAACSSTRIGGVSLPPYDSLNLGAHCGDNPDHVEENRKRLFAAGNLPSKPVWLEQVHGKDVLKLTGEPYASKRADASYSNTPGTVCAVMTADCLPVLFCNRAGTEVAAVHAGWRGLCAGVLEETVSCFADKPENILAWLGPAIGPRAFEVGAEVREAFMAVDAKASAAFIQHGDKYLADIYQLARQRLANVGVEQIFGGDRCTYTENETFFSYRRDKTTGRMASFIWLI 243
               SCOP domains d1xafa_ A: Hypothetical protein yfiH                                                                                                                                                                                                               SCOP domains
               CATH domains 1xafA00 A:2-243 CNF1/YfiH-like putative cysteine hydrolases                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.........eeeeee......................hhhhhhhhhhhhhhhhh...............eee............eeee.....eeeeee...eeeeeee.....eeeeeehhhhhhhhhhhhhhh....hhh.eeeee.........eeehhhhhhhhhhhhhhhh.eee...eeeehhhhhhhhhhhhhh..eeee.............hhhhhh....eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xaf A   2 SKLIVPQWPLPKGVAACSSTRIGGVSLPPYDSLNLGAHCGDNPDHVEENRKRLFAAGNLPSKPVWLEQVHGKDVLKLTGEPYASKRADASYSNTPGTVCAVmTADCLPVLFCNRAGTEVAAVHAGWRGLCAGVLEETVSCFADKPENILAWLGPAIGPRAFEVGAEVREAFmAVDAKASAAFIQHGDKYLADIYQLARQRLANVGVEQIFGGDRCTYTENETFFSYRRDKTTGRmASFIWLI 243
                                    11        21        31        41        51        61        71        81        91       101 |     111       121       131       141       151       161       171 |     181       191       201       211       221       231    |  241  
                                                                                                                               103-MSE                                                               173-MSE                                                        236-MSE

Chain B from PDB  Type:PROTEIN  Length:241
 aligned with Q83K13_SHIFL | Q83K13 from UniProtKB/TrEMBL  Length:243

    Alignment length:241
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242 
         Q83K13_SHIFL     3 KLIVPQWPLPKGVAACSSTRIGGVSLPPYDSLNLGAHCGDNPDHVEENRKRLFAAGNLPSKPVWLEQVHGKDVLKLTGEPYASKRADASYSNTPGTVCAVMTADCLPVLFCNRAGTEVAAVHAGWRGLCAGVLEETVSCFADKPENILAWLGPAIGPRAFEVGAEVREAFMAVDAKASAAFIQHGDKYLADIYQLARQRLANVGVEQIFGGDRCTYTENETFFSYRRDKTTGRMASFIWLI 243
               SCOP domains d1xafb_ B: Hypothetical protein yfiH                                                                                                                                                                                                              SCOP domains
               CATH domains 1xafB00 B:3-243 CNF1/YfiH-like putative cysteine hydrolases                                                                                                                                                                                       CATH domains
           Pfam domains (1) ----------------Cu-oxidase_4-1xafB01 B:19-242                                                                                                                                                                                                   - Pfam domains (1)
           Pfam domains (2) ----------------Cu-oxidase_4-1xafB02 B:19-242                                                                                                                                                                                                   - Pfam domains (2)
         Sec.struct. author .ee.........eeeeee......................hhhhhhhhhhhhhhhh.....ee.........eee............eeee.....eeeeee...eeeeeee.....eeeeeehhhhhhhhhhhhhhh....hhh.eeeee.........eeehhhhhhhhhhhhhhhh.eeee..eeeehhhhhhhhhhhhh...eeee.............hhhhhh....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xaf B   3 KLIVPQWPLPKGVAACSSTRIGGVSLPPYDSLNLGAHCGDNPDHVEENRKRLFAAGNLPSKPVWLEQVHGKDVLKLTGEPYASKRADASYSNTPGTVCAVmTADCLPVLFCNRAGTEVAAVHAGWRGLCAGVLEETVSCFADKPENILAWLGPAIGPRAFEVGAEVREAFmAVDAKASAAFIQHGDKYLADIYQLARQRLANVGVEQIFGGDRCTYTENETFFSYRRDKTTGRmASFIWLI 243
                                    12        22        32        42        52        62        72        82        92       102|      112       122       132       142       152       162       172|      182       192       202       212       222       232   |   242 
                                                                                                                              103-MSE                                                               173-MSE                                                        236-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: CNF1/YfiH-like putative cysteine hydrolases (10)

Superfamily: CNF1/YfiH-like putative cysteine hydrolases (10)

Family: YfiH-like (7)

Protein domain: Hypothetical protein yfiH (4)

Shigella flexneri [TaxId: 623] (2)

1a	d1xafa_	A:
1b	d1xafb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 4-Layer Sandwich (459)

Topology: CNF1/YfiH-like putative cysteine hydrolases (7)

Homologous Superfamily: CNF1/YfiH-like putative cysteine hydrolases (7)

2457t (Shigella flexneri 2a str) (1)

1a	1xafA00	A:2-243
1b	1xafB00	B:3-243

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Cu-oxidase_4] (6)

Family: Cu-oxidase_4 (6)

Shigella flexneri (2)

1a	Cu-oxidase_4-1xafB01	B:19-242
1b	Cu-oxidase_4-1xafB02	B:19-242

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q83K13_SHIFL | Q83K13)

molecular function
	GO:0046872		metal ion binding		Interacting selectively and non-covalently with any metal ion.

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
		ACT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ 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 ]
		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 ]

	Cis Peptide Bonds
		Asp A:32 - Ser A:33	[ RasMol ]
		Asp B:32 - Ser B:33	[ RasMol ]
		Pro A:29 - Pro A:30	[ RasMol ]
		Pro B:29 - Pro B:30	[ RasMol ]

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
	1xaf
		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
	Q83K13_SHIFL \| Q83K13
		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
	Q83K13_SHIFL \| Q83K13
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	Q83K13_SHIFL \| Q83K13	:	1u05

(no "Related Entries Specified in the PDB File" available for 1XAF)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 21)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (1, 1)

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