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(-) Description

Title :  JOINT NEUTRON AND X-RAY STRUCTURE OF DIISOPROPYL FLUOROPHOSPHATASE. DEUTERIUM OCCUPANCIES ARE 1-Q, WHERE Q IS OCCUPANCY OF H
 
Authors :  M. -M. Blum, M. Mustyakimov, H. Ruterjans, B. P. Schoenborn, P. Langan, H. Chen
Date :  15 Jan 08  (Deposition) - 27 Jan 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION; NEUTRON DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Keywords :  Beta-Propeller, Phosphotriesterase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. M. Blum, M. Mustyakimov, H. Ruterjans, K. Kehe, B. P. Schoenborn, P. Langan, J. C. Chen
Rapid Determination Of Hydrogen Positions And Protonation States Of Diisopropyl Fluorophosphatase By Joint Neutron An X-Ray Diffraction Refinement.
Proc. Natl. Acad. Sci. Usa V. 106 713 2009
PubMed-ID: 19136630  |  Reference-DOI: 10.1073/PNAS.0807842106

(-) Compounds

Molecule 1 - DIISOPROPYL-FLUOROPHOSPHATASE
    Chains: A
    EC Number: 3.1.8.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: SQUID
    Organism Scientific: LOLIGO VULGARIS
    Organism Taxid: 6622
    Synonym: DFPASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 248)

Asymmetric Unit (2, 248)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2DOD246Ligand/Ion
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2DOD-1Ligand/Ion

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:21 , ASN A:120 , ASN A:175 , ASP A:229 , DOD A:1032 , DOD A:1033 , DOD A:1034BINDING SITE FOR RESIDUE CA A 900
2AC2SOFTWAREASP A:232 , LEU A:273 , HIS A:274 , DOD A:1015 , DOD A:1052 , DOD A:1055BINDING SITE FOR RESIDUE CA A 901

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3BYC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BYC)

(-) 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:312
 aligned with DFPA_LOLVU | Q7SIG4 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:312
                                    12        22        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  
           DFPA_LOLVU     3 IPVIEPLFTKVTEDIPGAEGPVFDKNGDFYIVAPEVEVNGKPAGEILRIDLKTGKKTVICKPEVNGYGGIPAGCQCDRDANQLFVADMRLGLLVVQTDGTFEEIAKKDSEGRRMQGCNDCAFDYEGNLWITAPAGEVAPADYTRSMQEKFGSIYCFTTDGQMIQVDTAFQFPNGIAVRHMNDGRPYQLIVAETPTKKLWSYDIKGPAKIENKKVWGHIPGTHEGGADGMDFDEDNNLLVANWGSSHIEVFGPDGGQPKMRIRCPFEKPSNLHFKPQTKTIFVTEHENNAVWKFEWQRNGKKQYCETLKFGIF 314
               SCOP domains d3byca_ A: Diisopropylfluorophosphatase (phosphotriesterase, DFP)                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 3bycA00 A:3-314 TolB, C-terminal domain                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee....eeee......eeeee.....eeeee...ee..ee..eeeee......eeeee..ee..ee..eeeeee.....eeeeee...eeeeee....eee...............eeee.....eeeee..................eeeeee.....eeeeeeee..eeeeeeee.....eeeeeeee....eeeeeeeee..eeeeeeeeee.......eeeeeee.....eeeeee...eeeee........eeee.....eeeeee.....eeeeee....eeeeee.......hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3byc A   3 IPVIEPLFTKVTEDIPGAEGPVFDKNGDFYIVAPEVEVNGKPAGEILRIDLKTGKKTVICKPEVNGYGGIPAGCQCDRDANQLFVADMRLGLLVVQTDGTFEEIAKKDSEGRRMQGCNDCAFDYEGNLWITAPAGEVAPADYTRSMQEKFGSIYCFTTDGQMIQVDTAFQFPNGIAVRHMNDGRPYQLIVAETPTKKLWSYDIKGPAKIENKKVWGHIPGTHEGGADGMDFDEDNNLLVANWGSSHIEVFGPDGGQPKMRIRCPFEKPSNLHFKPQTKTIFVTEHENNAVWKFEWQRNGKKQYCETLKFGIF 314
                                    12        22        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
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (DFPA_LOLVU | Q7SIG4)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0047862    diisopropyl-fluorophosphatase activity    Catalysis of the reaction: diisopropyl fluorophosphate + H(2)O = diisopropyl phosphate + 2 H(+) + hydrogen fluoride.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DFPA_LOLVU | Q7SIG4: 1e1a 1pjx 2gvu 2gvv 2gvw 2gvx 2iao 2iap 2iaq 2iar 2ias 2iat 2iau 2iav 2iaw 2iax 3hlh 3hli 3i1c 3kgg 3li3 3li4 3li5 3o4p 3u0s 4o5s 4o5t

(-) Related Entries Specified in the PDB File

2gvw