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(-) Description

Title :  PSEUDOMONAS FLUORESCENS PHOX IN COMPLEX WITH PHOSPHATE
 
Authors :  S. C. Yong, P. Roversi, J. E. D. Lillington, O. B. Zeldin, E. F. Garman, S. B. C. Berks
Date :  02 Mar 12  (Deposition) - 13 Mar 13  (Release) - 17 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Beta-Propeller (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

(-) Compounds

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

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 29)

Asymmetric Unit (5, 29)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
2CL2Ligand/IonCHLORIDE ION
3EDO17Ligand/Ion1,2-ETHANEDIOL
4FEO2Ligand/IonMU-OXO-DIIRON
5PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3EDO10Ligand/Ion1,2-ETHANEDIOL
4FEO1Ligand/IonMU-OXO-DIIRON
5PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (3, 9)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3EDO7Ligand/Ion1,2-ETHANEDIOL
4FEO1Ligand/IonMU-OXO-DIIRON
5PO41Ligand/IonPHOSPHATE ION

(-) Sites  (29, 29)

Asymmetric Unit (29, 29)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU 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:1590 , CA A:1591 , CA A:1592 , FEO A:1593 , EDO A:1596 , HOH A:2153 , HOH A:2354 , HOH A:2553 , HOH A:2717BINDING SITE FOR RESIDUE PO4 A1589
02AC2SOFTWAREGLU A:273 , GLU A:387 , ASP A:479 , PO4 A:1589 , CA A:1591 , FEO A:1593 , HOH A:2152 , HOH A:2153 , HOH A:2636BINDING SITE FOR RESIDUE CA A1590
03AC3SOFTWAREGLU A:387 , ASP A:479 , ASP A:494 , PO4 A:1589 , CA A:1590 , HOH A:2553 , HOH A:2554BINDING SITE FOR RESIDUE CA A1591
04AC4SOFTWAREASP A:494 , GLU A:532 , PO4 A:1589 , HOH A:2188 , HOH A:2191 , HOH A:2652BINDING SITE FOR RESIDUE CA A1592
05AC5SOFTWAREGLU A:90 , CYS A:179 , GLU A:194 , GLU A:273 , ASP A:292 , GLU A:387 , PO4 A:1589 , CA A:1590 , HOH A:2153BINDING SITE FOR RESIDUE FEO A1593
06AC6SOFTWAREVAL A:390 , GLY A:482 , PHE A:483 , HOH A:2556 , HOH A:2638 , HOH A:2718 , HOH A:2719BINDING SITE FOR RESIDUE EDO A1595
07AC7SOFTWAREGLU A:90 , TYR A:91 , GLU A:194 , ASN A:195 , PO4 A:1589 , HOH A:2191 , HOH A:2333 , HOH A:2717BINDING SITE FOR RESIDUE EDO A1596
08AC8SOFTWAREASN A:93 , TYR A:96 , HIS A:551 , PRO A:552 , PRO A:569 , HOH A:2144 , HOH A:2145BINDING SITE FOR RESIDUE EDO A1597
09AC9SOFTWAREGLU A:251 , THR A:260 , ARG A:264 , HOH A:2428 , HOH A:2721BINDING SITE FOR RESIDUE EDO A1598
10BC1SOFTWAREGLY A:530 , GLY A:553 , ASN A:555 , GLY A:556 , GLY A:557BINDING SITE FOR RESIDUE CL A1599
11BC2SOFTWARESER A:456 , PRO A:471 , HOH A:2632 , HOH A:2722 , ALA B:18 , ASN B:499BINDING SITE FOR RESIDUE EDO A1600
12BC3SOFTWAREASN A:308 , HIS A:309 , ARG A:310 , ASP A:337 , SER A:467 , ASN A:468 , THR A:518 , GLY A:519 , HOH A:2674BINDING SITE FOR RESIDUE EDO A1601
13BC4SOFTWARESER A:497 , ASN A:508 , ILE A:529 , GLY A:530 , HOH A:2690BINDING SITE FOR RESIDUE EDO A1602
14BC5SOFTWARETHR A:323 , TYR A:325 , GLU A:347 , LYS A:352 , LYS A:442 , HOH A:2608 , ASN B:566BINDING SITE FOR RESIDUE EDO A1603
15BC6SOFTWARESER A:456 , PRO A:471 , MET A:474 , GLY A:505 , HOH A:2671 , HOH A:2672 , HOH A:2722 , HOH A:2724 , HOH A:2725BINDING SITE FOR RESIDUE EDO A1604
16BC7SOFTWAREPRO A:154 , GLN A:364 , HOH A:2493 , HOH A:2538 , HOH A:2727 , PRO B:565 , ASN B:566 , HOH B:2661BINDING SITE FOR RESIDUE EDO A1605
17BC8SOFTWAREGLU 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:1590 , CA B:1591 , CA B:1592 , FEO B:1593 , EDO B:1597 , HOH B:2143 , HOH B:2323 , HOH B:2514 , HOH B:2674BINDING SITE FOR RESIDUE PO4 B1589
18BC9SOFTWAREGLU B:273 , GLU B:387 , ASP B:479 , PO4 B:1589 , CA B:1591 , FEO B:1593 , HOH B:2142 , HOH B:2143 , HOH B:2592BINDING SITE FOR RESIDUE CA B1590
19CC1SOFTWAREGLU B:387 , ASP B:479 , ASP B:494 , PO4 B:1589 , CA B:1590 , HOH B:2514 , HOH B:2515BINDING SITE FOR RESIDUE CA B1591
20CC2SOFTWAREASP B:494 , GLU B:532 , PO4 B:1589 , HOH B:2171 , HOH B:2174 , HOH B:2607BINDING SITE FOR RESIDUE CA B1592
21CC3SOFTWAREGLU B:90 , CYS B:179 , GLU B:194 , GLU B:273 , ASP B:292 , GLU B:387 , PO4 B:1589 , CA B:1590 , HOH B:2143BINDING SITE FOR RESIDUE FEO B1593
22CC4SOFTWARELYS B:183 , LEU B:277 , HOH B:2313 , HOH B:2314 , HOH B:2517 , HOH B:2675BINDING SITE FOR RESIDUE EDO B1595
23CC5SOFTWARETRP B:38 , ASN B:93 , TYR B:96 , HIS B:551 , PRO B:552 , PRO B:569 , ARG B:570 , HOH B:2135 , HOH B:2136BINDING SITE FOR RESIDUE EDO B1596
24CC6SOFTWAREGLU B:90 , TYR B:91 , GLN B:177 , PO4 B:1589 , HOH B:2174 , HOH B:2306 , HOH B:2674BINDING SITE FOR RESIDUE EDO B1597
25CC7SOFTWAREGLY B:530 , GLY B:553 , ASN B:555 , GLY B:556 , GLY B:557BINDING SITE FOR RESIDUE CL B1598
26CC8SOFTWAREALA A:18 , ASN A:499 , HOH A:2024 , HOH A:2665 , HOH A:2724 , GLN B:472 , HOH B:2586 , HOH B:2589BINDING SITE FOR RESIDUE EDO B1599
27CC9SOFTWAREHIS B:43 , ARG B:141 , HOH B:2086 , HOH B:2256BINDING SITE FOR RESIDUE EDO B1600
28DC1SOFTWAREHOH A:2724 , ILE B:16 , PRO B:17 , GLN B:472 , ARG B:523 , HOH B:2020 , HOH B:2676 , HOH B:2677BINDING SITE FOR RESIDUE EDO B1601
29DC2SOFTWARELYS B:183 , HOH B:2675BINDING SITE FOR RESIDUE EDO B1602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ALF)

(-) Cis Peptide Bonds  (2, 2)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ALF)

(-) 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:581
 aligned with Q3K5N8_PSEPF | Q3K5N8 from UniProtKB/TrEMBL  Length:633

    Alignment length:581
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            633  
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624        |- 
         Q3K5N8_PSEPF    55 SRLLGFDSIPAATTDTISLPKGYKSSVLISWGQPLHKNGPAFDPSGNGTAAAQEVQFGDNNDGMSLFEFPGEKNRALMAINNEYTNYRYLYPHGGMPQSAEDVRKALACEGVSVIEVQRKNGQWQFVQGSRYNRRIHGNSPLRISGPAAGHELMKTSADKHGKKVLGTFQNCANGKTPWGTYLTCEENFTDCFGSSNAQQQFDPAQKRYGVSAASREINWHPFDPRFDMAKNPNELNRHGWVVEIDPFDPQSTPVKRTALGRFKHENAALAETDDGRAVVYMGDDERGEFIYKFVSRDKINHRNAKANRDILDHGTLYVARFDAGDGNPDHPKGQGQWIELTHGKNGIDASSGFADQAEVLIHARLAASVVGATRMDRPEWIVVSPKDGQVYCTLTNNAKRGEDGQPVGGPNPREKNVYGQILRWRTDRDDHASKTFAWDLFVVAGNPSVHAGTPKGGSSNITPQNMFNSPDGLGFDKAGRLWILTDGDSSNAGDFAGMGNNQMLCADPATGEIRRFMVGPIGCEVTGISFSPDQKTLFVGIQHPGENGGSTFPEHLPNGKPRSSVMAITREDGGIVGA--   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................eeeeeeee..................hhhhhh......eeeeeeee......eeeeeeee...hhhhhh..............hhhh.eeeeeeee......ee.......eeee...eeeee.....hhhhh........eee....eeeeee.....eeeee.hhhhhh.........hhhhhhhh.............hhhhh...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
                 4alf A   8 SRLLGFDSIPAATTDTISLPKGYKSSVLISWGQPLHKNGPAFDPSGNGTAAAQEVQFGDNNDGMSLFEFPGEKNRALMAINNEYTNYRYLYPHGGMPQSAEDVRKALACEGVSVIEVQRKNGQWQFVQGSRYNRRIHGNSPLRISGPAAGHELMKTSADKHGKKVLGTFQNCANGKTPWGTYLTCEENFTDCFGSSNAQQQFDPAQKRYGVSAASREINWHPFDPRFDMAKNPNELNRHGWVVEIDPFDPQSTPVKRTALGRFKHENAALAETDDGRAVVYMGDDERGEFIYKFVSRDKINHRNAKANRDILDHGTLYVARFDAGDGNPDHPKGQGQWIELTHGKNGIDASSGFADQAEVLIHARLAASVVGATRMDRPEWIVVSPKDGQVYCTLTNNAKRGEDGQPVGGPNPREKNVYGQILRWRTDRDDHASKTFAWDLFVVAGNPSVHAGTPKGGSSNITPQNMFNSPDGLGFDKAGRLWILTDGDSSNAGDFAGMGNNQMLCADPATGEIRRFMVGPIGCEVTGISFSPDQKTLFVGIQHPGENGGSTFPEHLPNGKPRSSVMAITREDGGIVGAHH 588
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587 


Chain B from PDB  Type:PROTEIN  Length:581
 aligned with Q3K5N8_PSEPF | Q3K5N8 from UniProtKB/TrEMBL  Length:633

    Alignment length:581
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            633  
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624        |- 
         Q3K5N8_PSEPF    55 SRLLGFDSIPAATTDTISLPKGYKSSVLISWGQPLHKNGPAFDPSGNGTAAAQEVQFGDNNDGMSLFEFPGEKNRALMAINNEYTNYRYLYPHGGMPQSAEDVRKALACEGVSVIEVQRKNGQWQFVQGSRYNRRIHGNSPLRISGPAAGHELMKTSADKHGKKVLGTFQNCANGKTPWGTYLTCEENFTDCFGSSNAQQQFDPAQKRYGVSAASREINWHPFDPRFDMAKNPNELNRHGWVVEIDPFDPQSTPVKRTALGRFKHENAALAETDDGRAVVYMGDDERGEFIYKFVSRDKINHRNAKANRDILDHGTLYVARFDAGDGNPDHPKGQGQWIELTHGKNGIDASSGFADQAEVLIHARLAASVVGATRMDRPEWIVVSPKDGQVYCTLTNNAKRGEDGQPVGGPNPREKNVYGQILRWRTDRDDHASKTFAWDLFVVAGNPSVHAGTPKGGSSNITPQNMFNSPDGLGFDKAGRLWILTDGDSSNAGDFAGMGNNQMLCADPATGEIRRFMVGPIGCEVTGISFSPDQKTLFVGIQHPGENGGSTFPEHLPNGKPRSSVMAITREDGGIVGA--   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................eeeeeeee..................hhhhhh......eeeeeeee......eeeeeeee...hhhhhh.............hhhhhheeeeeeee......ee.......eeee...eeeee..................eee....eeeeee.....eeeee.hhhhhh.........hhhhhhhh.............hhhhh...hhhhhhhh..eeee.........eee.hhh...eeeeeeee....eeeeeeee......eeeeeeeee....hhhhhhhhhh.eeeeeeee..........eeeeeeee........hhhhh..hhhhhhhhhhhhhhhhh......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
                 4alf B   8 SRLLGFDSIPAATTDTISLPKGYKSSVLISWGQPLHKNGPAFDPSGNGTAAAQEVQFGDNNDGMSLFEFPGEKNRALMAINNEYTNYRYLYPHGGMPQSAEDVRKALACEGVSVIEVQRKNGQWQFVQGSRYNRRIHGNSPLRISGPAAGHELMKTSADKHGKKVLGTFQNCANGKTPWGTYLTCEENFTDCFGSSNAQQQFDPAQKRYGVSAASREINWHPFDPRFDMAKNPNELNRHGWVVEIDPFDPQSTPVKRTALGRFKHENAALAETDDGRAVVYMGDDERGEFIYKFVSRDKINHRNAKANRDILDHGTLYVARFDAGDGNPDHPKGQGQWIELTHGKNGIDASSGFADQAEVLIHARLAASVVGATRMDRPEWIVVSPKDGQVYCTLTNNAKRGEDGQPVGGPNPREKNVYGQILRWRTDRDDHASKTFAWDLFVVAGNPSVHAGTPKGGSSNITPQNMFNSPDGLGFDKAGRLWILTDGDSSNAGDFAGMGNNQMLCADPATGEIRRFMVGPIGCEVTGISFSPDQKTLFVGIQHPGENGGSTFPEHLPNGKPRSSVMAITREDGGIVGAHH 588
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587
   Legend:   → Mismatch (orange background)
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  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)

(no "SCOP Domain" information available for 4ALF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

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.

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  Q3K5N8_PSEPF | Q3K5N8
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q3K5N8_PSEPF | Q3K5N8: 3zwu 4a9v 4a9x 4amf

(-) Related Entries Specified in the PDB File

3zwu PSEUDOMONAS FLUORESCENS PHOX IN COMPLEX WITH VANADATE, A TRANSITION STATE ANALOGUE
4a9v PSEUDOMONAS FLUORESCENS PHOX
4a9x PSEUDOMONAS FLUORESCENS PHOX IN COMPLEX WITH THE SUBSTRATE ANALOGUE APPCP