3ZWU - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   PSEUDOMONAS FLUORESCENS PHOX IN COMPLEX WITH VANADATE, A TRANSITION STATE ANALOGUE

Authors :   S. C. Yong, P. Roversi, J. E. D. Lillington, O. B. Zeldin, E. F. Garman, S. B. C. Berks

Date :   02 Aug 11 (Deposition) - 08 Aug 12 (Release) - 17 Sep 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.39

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

Keywords :   Hydrolase, Beta-Propeller, Iron (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. C. Yong, P. Roversi, J. Lillington, F. Rodriguez, M. Krehenbrink, O. B. Zeldin, E. F. Garman, S. M. Lea, B. C. Berks
A Complex Iron-Calcium Cofactor Catalyzing Phosphotransfer Chemistry
Science V. 345 1170 2014
PubMed-ID: 25190793 | Reference-DOI: 10.1126/SCIENCE.1254237

Molecule 1 - ALKALINE PHOSPHATASE PHOX
	Atcc	:	13525
	Chains	:	A, B
	EC Number	:	3.1.3.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE60-PHOX AND PREP4
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Variant	:	C43 DELTA TAT
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 48-633
	Organism Scientific	:	PSEUDOMONAS FLUORESCENS
	Organism Taxid	:	205922
	Strain	:	PF0-1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 14)

No.	Name	Count	Type	Full Name
1	CA	6	Ligand/Ion	CALCIUM ION
2	CL	4	Ligand/Ion	CHLORIDE ION
3	FEO	2	Ligand/Ion	MU-OXO-DIIRON
4	VO4	2	Ligand/Ion	VANADATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	FEO	1	Ligand/Ion	MU-OXO-DIIRON
4	VO4	1	Ligand/Ion	VANADATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	FEO	1	Ligand/Ion	MU-OXO-DIIRON
4	VO4	1	Ligand/Ion	VANADATE ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:90 , GLU A:194 , ASP A:292 , ARG A:385 , GLU A:387 , ASP A:479 , ASP A:494 , GLU A:532 , CA A:1591 , CA A:1592 , CA A:1593 , FEO A:1594 , HOH A:2196 , HOH A:2245 , HOH A:2481 , HOH A:2721 , HOH A:2910	BINDING SITE FOR RESIDUE VO4 A 700
02	AC2	SOFTWARE	GLY A:530 , GLY A:553 , ASN A:555 , GLY A:557	BINDING SITE FOR RESIDUE CL A1589
03	AC3	SOFTWARE	ARG A:328 , GLN A:344 , HOH A:2312 , HOH A:2317	BINDING SITE FOR RESIDUE CL A1590
04	AC4	SOFTWARE	GLU A:273 , GLU A:387 , ASP A:479 , VO4 A:700 , CA A:1592 , FEO A:1594 , HOH A:2195 , HOH A:2196 , HOH A:2815	BINDING SITE FOR RESIDUE CA A1591
05	AC5	SOFTWARE	GLU A:387 , ASP A:479 , ASP A:494 , VO4 A:700 , CA A:1591 , HOH A:2721 , HOH A:2722	BINDING SITE FOR RESIDUE CA A1592
06	AC6	SOFTWARE	ASP A:494 , GLU A:532 , VO4 A:700 , HOH A:2244 , HOH A:2252 , HOH A:2832	BINDING SITE FOR RESIDUE CA A1593
07	AC7	SOFTWARE	GLU A:90 , CYS A:179 , GLU A:194 , GLU A:273 , ASP A:292 , GLU A:387 , VO4 A:700 , CA A:1591 , HOH A:2196	BINDING SITE FOR RESIDUE FEO A1594
08	AC8	SOFTWARE	GLU B:90 , GLU B:194 , ASP B:292 , ARG B:385 , GLU B:387 , ASP B:479 , ASP B:494 , GLU B:532 , CA B:1591 , CA B:1592 , CA B:1593 , FEO B:1594 , HOH B:2180 , HOH B:2212 , HOH B:2407 , HOH B:2620 , HOH B:2798	BINDING SITE FOR RESIDUE VO4 B 700
09	AC9	SOFTWARE	GLY B:530 , GLY B:553 , ASN B:555 , GLY B:557	BINDING SITE FOR RESIDUE CL B1589
10	BC1	SOFTWARE	ARG B:328 , GLN B:344 , HOH B:2271 , HOH B:2274	BINDING SITE FOR RESIDUE CL B1590
11	BC2	SOFTWARE	GLU B:273 , GLU B:387 , ASP B:479 , VO4 B:700 , CA B:1592 , FEO B:1594 , HOH B:2179 , HOH B:2180 , HOH B:2706	BINDING SITE FOR RESIDUE CA B1591
12	BC3	SOFTWARE	GLU B:387 , ASP B:479 , ASP B:494 , VO4 B:700 , CA B:1591 , HOH B:2620 , HOH B:2621	BINDING SITE FOR RESIDUE CA B1592
13	BC4	SOFTWARE	ASP B:494 , GLU B:532 , VO4 B:700 , HOH B:2213 , HOH B:2217 , HOH B:2724	BINDING SITE FOR RESIDUE CA B1593
14	BC5	SOFTWARE	GLU B:90 , CYS B:179 , GLU B:194 , GLU B:273 , ASP B:292 , GLU B:387 , VO4 B:700 , CA B:1591 , HOH B:2180	BINDING SITE FOR RESIDUE FEO B1594

(no "SS Bond" information available for 3ZWU)

Asymmetric Unit

No.	Residues
1	Phe A:560	-	Pro A:561
2	Phe B:560	-	Pro B:561

(no "SAP(SNP)/Variant" information available for 3ZWU)

(no "PROSITE Motif" information available for 3ZWU)

(no "Exon" information available for 3ZWU)

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:580
 aligned with Q3K5N8_PSEPF | Q3K5N8 from UniProtKB/TrEMBL  Length:633

    Alignment length:580
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           633  
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       | -
         Q3K5N8_PSEPF    56 RLLGFDSIPAATTDTISLPKGYKSSVLISWGQPLHKNGPAFDPSGNGTAAAQEVQFGDNNDGMSLFEFPGEKNRALMAINNEYTNYRYLYPHGGMPQSAEDVRKALACEGVSVIEVQRKNGQWQFVQGSRYNRRIHGNSPLRISGPAAGHELMKTSADKHGKKVLGTFQNCANGKTPWGTYLTCEENFTDCFGSSNAQQQFDPAQKRYGVSAASREINWHPFDPRFDMAKNPNELNRHGWVVEIDPFDPQSTPVKRTALGRFKHENAALAETDDGRAVVYMGDDERGEFIYKFVSRDKINHRNAKANRDILDHGTLYVARFDAGDGNPDHPKGQGQWIELTHGKNGIDASSGFADQAEVLIHARLAASVVGATRMDRPEWIVVSPKDGQVYCTLTNNAKRGEDGQPVGGPNPREKNVYGQILRWRTDRDDHASKTFAWDLFVVAGNPSVHAGTPKGGSSNITPQNMFNSPDGLGFDKAGRLWILTDGDSSNAGDFAGMGNNQMLCADPATGEIRRFMVGPIGCEVTGISFSPDQKTLFVGIQHPGENGGSTFPEHLPNGKPRSSVMAITREDGGIVGA--   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeeee..................hhhhhh......eeeeeeeee..eeeeeeeeeee...hhhhhh.......hhhhhhhhhhhheeeeeeeeee..eeee.......eeee...eeeee.....hhhhh........eee....eeeeee.....eeeee.hhhhhh.........hhhhhhh..............hhhh....hhhhhhhh..eeee.........eee.hhh.......eeee....eeeeeee.......eeeeeeeee....hhhhhhhhhh.eeeeeeee..........eeeeeeee........hhhhh..hhhhhhhhhhhhhhhh.......eeeeee......eeeee.........................eeeeeee.hhh....eeeeeeeee.........hhhhh............eeeeee.....eeeee......hhhhh.....eeeee......eeeeee.....eeeeeee.....eeeeeee.....................eeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zwu A   9 RLLGFDSIPAATTDTISLPKGYKSSVLISWGQPLHKNGPAFDPSGNGTAAAQEVQFGDNNDGMSLFEFPGEKNRALMAINNEYTNYRYLYPHGGMPQSAEDVRKALACEGVSVIEVQRKNGQWQFVQGSRYNRRIHGNSPLRISGPAAGHELMKTSADKHGKKVLGTFQNCANGKTPWGTYLTCEENFTDCFGSSNAQQQFDPAQKRYGVSAASREINWHPFDPRFDMAKNPNELNRHGWVVEIDPFDPQSTPVKRTALGRFKHENAALAETDDGRAVVYMGDDERGEFIYKFVSRDKINHRNAKANRDILDHGTLYVARFDAGDGNPDHPKGQGQWIELTHGKNGIDASSGFADQAEVLIHARLAASVVGATRMDRPEWIVVSPKDGQVYCTLTNNAKRGEDGQPVGGPNPREKNVYGQILRWRTDRDDHASKTFAWDLFVVAGNPSVHAGTPKGGSSNITPQNMFNSPDGLGFDKAGRLWILTDGDSSNAGDFAGMGNNQMLCADPATGEIRRFMVGPIGCEVTGISFSPDQKTLFVGIQHPGENGGSTFPEHLPNGKPRSSVMAITREDGGIVGAHH 588
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588

Chain B from PDB  Type:PROTEIN  Length:580
 aligned with Q3K5N8_PSEPF | Q3K5N8 from UniProtKB/TrEMBL  Length:633

    Alignment length:580
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           633  
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       | -
         Q3K5N8_PSEPF    56 RLLGFDSIPAATTDTISLPKGYKSSVLISWGQPLHKNGPAFDPSGNGTAAAQEVQFGDNNDGMSLFEFPGEKNRALMAINNEYTNYRYLYPHGGMPQSAEDVRKALACEGVSVIEVQRKNGQWQFVQGSRYNRRIHGNSPLRISGPAAGHELMKTSADKHGKKVLGTFQNCANGKTPWGTYLTCEENFTDCFGSSNAQQQFDPAQKRYGVSAASREINWHPFDPRFDMAKNPNELNRHGWVVEIDPFDPQSTPVKRTALGRFKHENAALAETDDGRAVVYMGDDERGEFIYKFVSRDKINHRNAKANRDILDHGTLYVARFDAGDGNPDHPKGQGQWIELTHGKNGIDASSGFADQAEVLIHARLAASVVGATRMDRPEWIVVSPKDGQVYCTLTNNAKRGEDGQPVGGPNPREKNVYGQILRWRTDRDDHASKTFAWDLFVVAGNPSVHAGTPKGGSSNITPQNMFNSPDGLGFDKAGRLWILTDGDSSNAGDFAGMGNNQMLCADPATGEIRRFMVGPIGCEVTGISFSPDQKTLFVGIQHPGENGGSTFPEHLPNGKPRSSVMAITREDGGIVGA--   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeeee..................hhhhhh......eeeeeeeee..eeeeeeeeeee...hhhhhh.......hhhhhhhhhhhheeeeeeeeee..eeee.......eeee...eeeee.....hhhhh........eee....eeeeee.....eeeee.hhhhhh.........hhhhhhh..............hhhh....hhhhhhhh..eeee.........eee.hhh.......eeee....eeeeeee.......eeeeeeeee....hhhhhhhhhh.eeeeeeee..........eeeeeeee........hhhhh..hhhhhhhhhhhhhhhh.......eeeeee......eeeee.........................eeeeeee.hhh....eeeeeeeee.........hhhhh............eeeeee.....eeeee......hhhhh.....eeeee......eeeeee.....eeeeeee.....eeeeeee.....................eeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zwu B   9 RLLGFDSIPAATTDTISLPKGYKSSVLISWGQPLHKNGPAFDPSGNGTAAAQEVQFGDNNDGMSLFEFPGEKNRALMAINNEYTNYRYLYPHGGMPQSAEDVRKALACEGVSVIEVQRKNGQWQFVQGSRYNRRIHGNSPLRISGPAAGHELMKTSADKHGKKVLGTFQNCANGKTPWGTYLTCEENFTDCFGSSNAQQQFDPAQKRYGVSAASREINWHPFDPRFDMAKNPNELNRHGWVVEIDPFDPQSTPVKRTALGRFKHENAALAETDDGRAVVYMGDDERGEFIYKFVSRDKINHRNAKANRDILDHGTLYVARFDAGDGNPDHPKGQGQWIELTHGKNGIDASSGFADQAEVLIHARLAASVVGATRMDRPEWIVVSPKDGQVYCTLTNNAKRGEDGQPVGGPNPREKNVYGQILRWRTDRDDHASKTFAWDLFVVAGNPSVHAGTPKGGSSNITPQNMFNSPDGLGFDKAGRLWILTDGDSSNAGDFAGMGNNQMLCADPATGEIRRFMVGPIGCEVTGISFSPDQKTLFVGIQHPGENGGSTFPEHLPNGKPRSSVMAITREDGGIVGAHH 588
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588

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 '\|'

(no "SCOP Domain" information available for 3ZWU)

(no "CATH Domain" information available for 3ZWU)

(no "Pfam Domain" information available for 3ZWU)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q3K5N8_PSEPF | Q3K5N8)

molecular function
	GO:0046872		metal ion binding		Interacting selectively and non-covalently with any metal ion.
	GO:0000166		nucleotide binding		Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Phe A:560 - Pro A:561	[ RasMol ]
		Phe B:560 - Pro B:561	[ RasMol ]

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	3zwu
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	Q3K5N8_PSEPF \| Q3K5N8	:	4a9v 4a9x 4alf 4amf

(no "Related Entries Specified in the PDB File" available for 3ZWU)

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (4, 14)

Sites (14, 14)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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