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(-) Description

Title :  CRYSTAL STRUCTURE OF PROBABLE P-NITROPHENYL PHOSPHATASE (PHO2) (TARGET EFI-501307) FROM ARCHAEOGLOBUS FULGIDUS DSM 4304 WITH MAGNESIUM BOUND
 
Authors :  Y. Patskovsky, R. Toro, R. Bhosle, B. Hillerich, R. D. Seidel, E. Washin A. Scott Glenn, S. Chowdhury, B. Evans, J. Hammonds, W. D. Zencheck, H N. Al Obaidi, M. Stead, J. Love, K. N. Allen, D. Dunaway-Mariano, J. A. S. C. Almo, Enzyme Function Initiative (Efi)
Date :  25 Feb 13  (Deposition) - 06 Mar 13  (Release) - 06 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Magnesium Binding, Structural Genomics, Enzyme Function Initiative (Efi) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, R. Toro, R. Bhosle, B. Hillerich, R. D. Seidel, E. Washington, A. Scott Glenn, S. Chowdhury, B. Evans, J. Hammonds, W. D. Zencheck, H. J. Imker, N. F. Al Obaidi, M. Stead, J. Love, K. N. Allen, D. Dunaway-Mariano, J. A. Gerlt, S. C. Almo
Crystal Structure Of Probable P-Nitrophenyl Phosphatase Fro Archaeoglobus Fulgidus.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - P-NITROPHENYL PHOSPHATASE (PHO2)
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: AF_0374
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 224325
    Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1CL8Ligand/IonCHLORIDE ION
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:11 , ASP A:13 , ASP A:209 , HOH A:401 , HOH A:402 , HOH A:403BINDING SITE FOR RESIDUE MG A 301
02AC2SOFTWARESER A:44 , ASN A:46 , HOH A:429 , HOH A:503BINDING SITE FOR RESIDUE CL A 302
03AC3SOFTWAREASN A:46 , ARG A:49 , ARG A:57BINDING SITE FOR RESIDUE CL A 303
04AC4SOFTWAREASN A:148 , GLY A:162 , THR A:163 , HOH A:491BINDING SITE FOR RESIDUE CL A 304
05AC5SOFTWARELYS A:34 , LEU A:63 , GLU A:64 , HOH A:568BINDING SITE FOR RESIDUE CL A 305
06AC6SOFTWAREASP B:11 , ASP B:13 , ASP B:209 , HOH B:401 , HOH B:402 , HOH B:403BINDING SITE FOR RESIDUE MG B 301
07AC7SOFTWARESER B:44 , ASN B:46 , HOH B:423BINDING SITE FOR RESIDUE CL B 302
08AC8SOFTWAREASN B:46 , ARG B:49 , ARG B:57 , HOH B:530BINDING SITE FOR RESIDUE CL B 303
09AC9SOFTWAREASN B:148 , GLY B:162 , THR B:163BINDING SITE FOR RESIDUE CL B 304
10BC1SOFTWAREARG B:49 , SER B:50 , ILE B:53 , GLY B:97 , HOH B:586 , HOH B:591BINDING SITE FOR RESIDUE CL B 305

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:184 -Pro A:185
2Lys B:184 -Pro B:185

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JDP)

(-) Sequences/Alignments

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:264
                                                                                                                                                                                                                                                                                                        
               SCOP domains d4jdpa_ A: automated matches                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee......ee..eehhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhh....hhh.eeehhhhhhhhhhhhh...eeee..hhhhhhhhhhh..ee.......eeee......hhhhhhhhhhhhhhh.eeee.....eeee..eeee.hhhhhhhhhhhhh....ee....hhhhhhhhhhhhh.hhh.eeeee....hhhhhhhhh..eeeee........hhhhhhhhhh....eee.hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jdp A   1 MMPDKKGYIIDIDGVIGKSVTPIPEGVEGVKKLKELGKKIIFVSNNSTRSRRILLERLRSFGLEVGEDEILVATYATARFIAREKPNAKVFTTGEEGLIEELRLAGLEIVDYDEAEYLVVGSNRKINFELMTKALRACLRGIRYIATNPDRIFPAEDGPIPGTGMIIGALYWMTGREPDVVVGKPSEVIMREALDILGLDAKDVAVVGDQIDVDVAAGKAIGAETVLVLTGVTTRENLDQMIERHGLKPDYVFNSLKDMVEALE 264
                                    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    


Chain B from PDB  Type:PROTEIN  Length:265
                                                                                                                                                                                                                                                                                                         
               SCOP domains d4jdpb_ B: automated matches                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee......ee..eehhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhh....hhh.eeehhhhhhhhhhhhh...eeee..hhhhhhhhhhh..ee.......eeee......hhhhhhhhhhhhhh..eeee.....ee......ee.hhhhhhhhhhhhh....ee....hhhhhhhhhhhhh.hhh.eeeee....hhhhhhhhh..eeeee........hhhhhhhhhh....eee.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jdp B  -1 QSMMPDKKGYIIDIDGVIGKSVTPIPEGVEGVKKLKELGKKIIFVSNNSTRSRRILLERLRSFGLEVGEDEILVATYATARFIAREKPNAKVFTTGEEGLIEELRLAGLEIVDYDEAEYLVVGSNRKINFELMTKALRACLRGIRYIATNPDRIFPAEDGPIPGTGMIIGALYWMTGREPDVVVGKPSEVIMREALDILGLDAKDVAVVGDQIDVDVAAGKAIGAETVLVLTGVTTRENLDQMIERHGLKPDYVFNSLKDMVEAL 263
                                     8        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
   Legend:   → Mismatch (orange background)
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    → 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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Lys A:184 - Pro A:185   [ RasMol ]  
    Lys B:184 - Pro B:185   [ RasMol ]  
 

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