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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHOSERINE PHOSPHATASE SERB FROM MYCOBACTERIUM AVIUM, NATIVE FORM
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  15 Oct 10  (Deposition) - 10 Nov 10  (Release) - 11 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Ssgcid, Phosphoserine Phosphatase Serb, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Abendroth, A. S. Gardberg, J. I. Robinson, J. S. Christensen, B. L. Staker, P. J. Myler, L. J. Stewart, T. E. Edwards
Sad Phasing Using Iodide Ions In A High-Throughput Structural Genomics Environment.
J. Struct. Funct. Genom. V. 12 83 2011
PubMed-ID: 21359836  |  Reference-DOI: 10.1007/S10969-011-9101-7
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOSERINE PHOSPHATASE SERB
    ChainsA
    EC Number3.1.3.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidAVA0421
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneSERB, MAV_3907
    Organism ScientificMYCOBACTERIUM AVIUM
    Organism Taxid243243
    Strain104

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:187 , ASP A:189 , ASP A:343 , HOH A:429 , HOH A:440 , HOH A:451BINDING SITE FOR RESIDUE MG A 412
2AC2SOFTWAREASP A:187 , GLY A:276 , LYS A:320 , ASN A:346 , HOH A:440 , HOH A:461BINDING SITE FOR RESIDUE CL A 413
3AC3SOFTWAREASP A:189 , ARG A:232 , GLY A:277 , HOH A:502BINDING SITE FOR RESIDUE EDO A 414

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P96)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Arg A:105 -Pro A:106
2Tyr A:135 -Pro A:136
3Gly A:312 -Pro A:313

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P96)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ACTPS51671 ACT domain profile.SERB_MYCA110-88  1A:10-88
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ACTPS51671 ACT domain profile.SERB_MYCA110-88  2A:10-88

(-) Exons   (0, 0)

(no "Exon" information available for 3P96)

(-) 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:396
 aligned with SERB_MYCA1 | A0QJI1 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:396
                                    14        24        34        44        54        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      
           SERB_MYCA1     5 PKVSVLITVTGVDQPGVTATLFEVLSGHGVELLNVEQVVIRHRLTLGVLVCCPADVADGPALRHDVEAAIRKVGLDVSIERSDDVPIIREPSTHTIFVLGRPITAAAFGAVAREVAALGVNIDLIRGVSDYPVIGLELRVSVPPGADGALRTALNRVSSEEHVDVAVEDYTLERRAKRLIVFDVDSTLVQGEVIEMLAAKAGAEGQVAAITDAAMRGELDFAQSLQQRVATLAGLPATVIDEVAGQLELMPGARTTLRTLRRLGYACGVVSGGFRRIIEPLAEELMLDYVAANELEIVDGTLTGRVVGPIIDRAGKATALREFAQRAGVPMAQTVAVGDGANDIDMLAAAGLGIAFNAKPALREVADASLSHPYLDTVLFLLGVTRGEIEAADAID 400
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---ACT_6-3p96A01 A:8-84                                                         ---------------------------------------------------------------------------------------------------HAD-3p96A02 A:184-352                                                                                                                                                    ------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeee...hhhhhhhhhhh....eeeeeeeeee..eeeeeeeeeehhhhhhhhhhhhhhhhhhhhh..eeeeee............eeeeeee...hhhhhhhhhhhhhhh..eeeeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhh.eeeeee.........eeee.........hhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhhhhhhh....hhhhhhhhhhhh..eeeeeeeeehhhhhhhhhhh...eeeee.eeee..eeeeee.....hhhhhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh.eeeee..hhhhhhhh.eee.....hhhhhhh..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----ACT  PDB: A:10-88 UniProt: 10-88                                               ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p96 A   5 PKVSVLITVTGVDQPGVTATLFEVLSRHGVELLNVEQVVIRHRLTLGVLVCCPADVADGPALRHDVEAAIRKVGLDVSIERSDDVPIIREPSTHTIFVLGRPITAAAFGAVAREVAALGVNIDLIRGVSDYPVIGLELRVSVPPGADEALRTALNRVSSEEHVDVAVEDYTLERRAKRLIVFDVDSTLVQGEVIEMLAAKAGAEGQVAAITDAAMRGELDFAQSLQQRVATLAGLPATVIDEVAGQLELMPGARTTLRTLRRLGYACGVVSGGFRRIIEPLAEELMLDYVAANELEIVDGTLTGRVVGPIIDRAGKATALREFAQRAGVPMAQTVAVGDGANDIDMLAAAGLGIAFNAKPALREVADASLSHPYLDTVLFLLGVTRGEIEAADAID 400
                                    14        24        34        44        54        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      

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3P96)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P96)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: ACT (34)
(-)
Clan: HAD (186)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (SERB_MYCA1 | A0QJI1)
molecular function
    GO:0016597    amino acid binding    Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0004647    phosphoserine phosphatase activity    Catalysis of the reaction: L(or D)-O-phosphoserine + H2O = L(or D)-serine + phosphate.
biological process
    GO:0006564    L-serine biosynthetic process    The chemical reactions and pathways resulting in the formation of L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SERB_MYCA1 | A0QJI15is2 5it0 5it4 5jjb 5jlp 5jlr 5jma 5t41

(-) Related Entries Specified in the PDB File

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