1Q35 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF PASTEURELLA HAEMOLYTICA APO FERRIC ION-BINDING PROTEIN A

Authors :   S. R. Shouldice, D. R. Dougan, R. J. Skene, G. Snell, D. Scheibe, P. A. Williams, S. Kirby, D. E. Mcree, A. B. Schryvers, L. W. Tari

Date :   28 Jul 03 (Deposition) - 11 Nov 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.20

Chains :   Asym./Biol. Unit : A

Keywords :   Iron Binding Protein, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. R. Shouldice, D. R. Dougan, P. A. Williams, R. J. Skene, G. Snell, D. Scheibe, S. Kirby, D. J. Hosfield, D. E. Mcree, A. B. Schryvers, L. W. Tari
Crystal Structure Of Pasteurella Haemolytica Ferric Ion-Binding Protein A Reveals A Novel Class Of Bacterial Iron-Binding Proteins
J. Biol. Chem. V. 278 41093 2003
PubMed-ID: 12882966 | Reference-DOI: 10.1074/JBC.M306821200
(for further references see the PDB file header)

Molecule 1 - IRON BINDING PROTEIN FBPA
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PT7-7
	Expression System Strain	:	BL21(DE3)/PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	FBPA
	Organism Scientific	:	MANNHEIMIA HAEMOLYTICA
	Organism Taxid	:	75985
	Synonym	:	FERRIC ION-BINDING PROTEIN A

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	FMT	2	Ligand/Ion	FORMIC ACID

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:61 , GLU A:65 , ALA A:298 , HOH A:1198 , HOH A:1261 , HOH A:1337 , HOH A:1400	BINDING SITE FOR RESIDUE EDO A 1003
2	AC2	SOFTWARE	ARG A:10 , LEU A:14 , VAL A:58 , ARG A:101 , TYR A:142 , TYR A:198 , HOH A:1164	BINDING SITE FOR RESIDUE FMT A 1001
3	AC3	SOFTWARE	ARG A:136 , GLY A:177 , ASP A:178 , ARG A:179 , TYR A:199 , HOH A:1020 , HOH A:1172	BINDING SITE FOR RESIDUE FMT A 1002

Asymmetric/Biological Unit

No.	Residues
1	A:134	-	A:190

Asymmetric/Biological Unit

No.	Residues
1	Gly A:38	-	Leu A:39

(no "SAP(SNP)/Variant" information available for 1Q35)

(no "PROSITE Motif" information available for 1Q35)

(no "Exon" information available for 1Q35)

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:317
 aligned with Q9Z4N6_MANHA | Q9Z4N6 from UniProtKB/TrEMBL  Length:342

    Alignment length:318
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332        
         Q9Z4N6_MANHA    23 ANEVNVYSYRQPYLIEPMLKNFEKDTGIKVNIIFADKGLVDRVKQEGELSPADVLLTVDISRVMEIVNADLAQKIDSKVLEKNIPAQFRDSNDQWFGLTTRARVIYTSKDRVGKLPAGFDYLDLAKPEYKGKVCVRSGKNSYNVSLFAAMIEHYGIEKTKAFLEGLKANLARKPQGGDRDQVKAIKEGICDYSIGNSYYYGKMLDDEKQKSWAEAAIINFPSGEHGTHKNISGVVIAKHSPNKANAVKLIEYLSGEKAQGLYAELNHEYPVKEGIEPSAIVKGWGTFKSDTIKLEDIAKNYEAALKLVDEVKFDDFSE 340
               SCOP domains d1q35a_ A: Ferric-binding protein Fb pA                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1q35A01 A:1-98,A:227-275 Periplasmic  binding protein-like II                                     1q35A02 A:99-226,A:276-318 Periplasmic binding protein-like II                                                                  1q35A01 A:1-98,A:227-275                         1q35A02 A:99-226,A:276-318                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhhhh.eeeeee..-.hhhhhhhhhhhh...eeee.hhhhhhhhhhh.......hhhhhhhhhhhhh......eeeeeeeeeeeee...........hhhhhhhhhhh..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh....eeeeehhhhhhhhhh..hhhhhhheeee........eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh.ee.......hhhhhhh........hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1q35 A   1 ANEVNVYSYRQPYLIEPMLKNFEKDTGIKVNIIFAD-GLVDRVKQEGELSPADVLLTVDISRVMEIVNADLAQKIDSKVLEKNIPAQFRDSNDQWFGLTTRARVIYTSKDRVGKLPAGFDYLDLAKPEYKGKVCVRSGKNSYNVSLFAAMIEHYGIEKTKAFLEGLKANLARKPQGGDRDQVKAIKEGICDYSIGNSYYYGKMLDDEKQKSWAEAAIINFPSGEHGTHKNISGVVIAKHSPNKANAVKLIEYLSGEKAQGLYAELNHEYPVKEGIEPSAIVKGWGTFKSDTIKLEDIAKNYEAALKLVDEVKFDDFSE 318
                                    10        20        30     | |40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310        
                                                              36 |                                                                                                                                                                                                                                                                                        
                                                                38

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) (23833)

Fold: Periplasmic binding protein-like II (813)

Superfamily: Periplasmic binding protein-like II (813)

Family: Phosphate binding protein-like (463)

Protein domain: Ferric-binding protein FbpA (25)

Mannheimia haemolytica [TaxId: 75985] (3)

d1q35a_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: D-Maltodextrin-Binding Protein; domain 2 (600)

Homologous Superfamily: Periplasmic binding protein-like II (486)

Mannheimia haemolytica. Organism_taxid: 75985. (3)

1a	1q35A01	A:1-98,A:227-275
1b	1q35A02	A:99-226,A:276-318

(no "Pfam Domain" information available for 1Q35)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q9Z4N6_MANHA | Q9Z4N6)

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
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FMT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
		Gly A:38 - Leu A:39	[ 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
	1q35
		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
	Q9Z4N6_MANHA \| Q9Z4N6
		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
	Q9Z4N6_MANHA \| Q9Z4N6
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	Q9Z4N6_MANHA \| Q9Z4N6	:	1si0 1si1

(no "Related Entries Specified in the PDB File" available for 1Q35)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (1, 1)

Cis Peptide Bonds (1, 1)

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 (1, 2)

Pfam Domains (0, 0)

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