4F1V - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   SUBATOMIC RESOLUTION STRUCTURE OF A HIGH AFFINITY PERIPLASMIC PHOSPHATE-BINDING PROTEIN (PFLUDING) BOUND WITH PHOSPHATE AT PH 8.5

Authors :   D. Liebschner, M. Elias, D. S. Tawfik, S. Moniot, B. Fournier, K. Scott, B. Guillot, C. Lecomte, E. Chabriere

Date :   07 May 12 (Deposition) - 23 May 12 (Release) - 21 Nov 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   0.88

Chains :   Asym./Biol. Unit : A

Keywords :   Venus Flytrap, Phosphate Binding Protein, Psts, Ding, Phosphate- Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Elias, A. Wellner, K. Goldin-Azulay, E. Chabriere, J. A. Vorholt, T. J. Erb, D. S. Tawfik
The Molecular Basis Of Phosphate Discrimination In Arsenate-Rich Environments.
Nature V. 491 134 2012
PubMed-ID: 23034649 | Reference-DOI: 10.1038/NATURE11517
(for further references see the PDB file header)

Molecule 1 - PUTATIVE ALKALINE PHOSPHATASE
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	PFLU_2427
	Organism Scientific	:	PSEUDOMONAS FLUORESCENS
	Organism Taxid	:	216595
	Strain	:	SBW25

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	PI	1	Ligand/Ion	HYDROGENPHOSPHATE ION
2	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:1007 , THR A:1008 , LEU A:1009 , GLY A:1031 , SER A:1032 , ASP A:1062 , ARG A:1141 , SER A:1145 , GLY A:1146 , THR A:1147	BINDING SITE FOR RESIDUE PI A 1401
2	AC2	SOFTWARE	LYS A:1158 , HOH A:2182 , HOH A:2266 , HOH A:2332 , HOH A:2347 , HOH A:2869 , HOH A:2999 , HOH A:3122	BINDING SITE FOR RESIDUE SO4 A 1402

Asymmetric/Biological Unit

No.	Residues
1	A:1114	-	A:1159
2	A:1300	-	A:1363

(no "Cis Peptide Bond" information available for 4F1V)

(no "SAP(SNP)/Variant" information available for 4F1V)

(no "PROSITE Motif" information available for 4F1V)

(no "Exon" information available for 4F1V)

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:372
                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4f1va_ A: Phosphate-binding protein                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee...hhhhhh............ee.hhhhhhhhhhhhhhhhh..........eeee....hhhhhhhhhhhhhhhhh.eeeeeeeeee....ee.......eehhhhhhhhhhh...hhhhh.........eeeee...hhhhhhhhhhhhhhh...........hhhhh.........eeehhhhhhhhhhh....ee..........hhhhhhh.....ee..hhhhh......hhhhhhhhhhh....hhhhh.hhhhhh..ee.......ee........eeeeeeeee....hhhhhhhhhhhhhhhh.....hhhhhhhh.....hhhhhhhhhhhhh...................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4f1v A 1000 MDINGGGATLPQALYQTSGVLTAGFAQYIGVGSGNGKAAFLNNDYTKFQAGVTNKNVHWAGSDSKLSATELSTYASAKQPTWGKLIQVPSVGTSVAIPFNKSGSAAVDLSVQELCGVFSGRINTWDGISGSGRTGPIVVVYRSESSGTTELFTRFLNAKCNAETGNFAVTTTFGTSFSGGLPAGAVAATGSQGVMTALAAGDGRITYMSPDFAAPTLAGLDDATKVARVGKNVATNTQGVSPAAANVSAAIGAVPVPAAADRSNPDAWVPVFGPDNTAGVQPYPTSGYPILGFTNLIFSQCYADATQTTQVRDFFTKHYGASNNNDAAITANAFVPLPTAWKATVRASFLTASNALSIGNTNVCNGIGRPLL 1371
                                  1009      1019      1029      1039      1049      1059      1069      1079      1089      1099      1109      1119      1129      1139      1149      1159      1169      1179      1189      1199      1209      1219      1229      1239      1249      1259      1269      1279      1289      1299      1309      1319      1329      1339      1349      1359      1369

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: Phosphate-binding protein (19)

Pseudomonas fluorescens [TaxId: 216595] (1)

d4f1va_

(no "CATH Domain" information available for 4F1V)

(no "Pfam Domain" information available for 4F1V)

Asymmetric/Biological Unit(hide GO term definitions)

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
		PI	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4f1v)

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
	4f1v
		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
	C3K8K1_PSEFS \| C3K8K1
		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
	C3K8K1_PSEFS \| C3K8K1
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	C3K8K1_PSEFS \| C3K8K1	:	4f18 4f19 4f1u

2q9t	THE SAME PROTEIN AT LOWER RESOLUTION.
4f18	THE SAME PROTEIN BOUND WITH ARSENATE AT 0.96A RESOLUTION AND PH 8.5
4f19	THE SAME PROTEIN BOUND WITH ARSENATE AT 0.95A RESOLUTION AND PH 4.5

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

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 (0, 0)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

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