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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PHOSPHATASE SC4828 WITH THE NON-HYDROLYZABLE NUCLEOTIDE GPCP
 
Authors :  A. U. Singer, X. Xu, H. Zheng, A. Joachimiak, A. M. Edwards, A. Savchenko A. F. Yakunin, Midwest Center For Structural Genomics (Mcsg)
Date :  16 Oct 08  (Deposition) - 09 Dec 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Nucleoside Diphosphatase, Gdp/Udp'Ase, Streptomyces, Non-Hydrolysable Gdp Analogue, Lipocalcin Fold, Metalloprotein, Hydrolase, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Proudfoot, M. Brown, A. U. Singer, M. -C. Jobin, X. Xu, H. Zheng, C. Chang, A. M. Edwards, A. Joachimiak, A. Savchenko, A. F. Yakunin
Structure And Mechanism Of A New Family Of Prokaryotic Nucleoside Diphosphatases.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHOSPHATASE SC4828
    Atcc: BAA-471
    Chains: A
    EC Number: 3.6.1.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15TVLIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SCO5041, SCK7.14, SCK7.14C
    Organism Scientific: STREPTOMYCES COELICOLOR A3(2)
    Organism Taxid: 100226
    Strain: A3(2) / M145

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2GOL1Ligand/IonGLYCEROL
3GP21Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID GUANOSYL ESTER
4NA2Ligand/IonSODIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:133 , ASP A:149 , ASP A:153 , GP2 A:401 , HOH A:522BINDING SITE FOR RESIDUE CA A 301
2AC2SOFTWAREPHE A:151 , ASP A:153 , ASP A:166 , GP2 A:401 , HOH A:582 , HOH A:818BINDING SITE FOR RESIDUE CA A 302
3AC3SOFTWAREASP A:166 , GP2 A:401 , HOH A:664 , HOH A:735 , HOH A:828 , HOH A:829BINDING SITE FOR RESIDUE CA A 303
4AC4SOFTWAREASP A:98 , HOH A:550 , HOH A:733 , HOH A:753 , HOH A:754 , HOH A:755BINDING SITE FOR RESIDUE NA A 304
5AC5SOFTWARETRP A:130 , PRO A:204 , PHE A:205 , GLY A:208 , TRP A:209 , GLU A:210BINDING SITE FOR RESIDUE NA A 305
6AC6SOFTWARETRP A:100 , PHE A:101 , THR A:103 , TYR A:131 , ASN A:133 , ASP A:149 , ASP A:153 , ARG A:165 , ASP A:166 , CA A:301 , CA A:302 , CA A:303 , HOH A:508 , HOH A:512 , HOH A:546 , HOH A:593 , HOH A:601 , HOH A:664 , HOH A:667 , HOH A:673 , HOH A:735 , HOH A:772 , HOH A:774 , HOH A:794 , HOH A:818 , HOH A:821 , HOH A:822BINDING SITE FOR RESIDUE GP2 A 401
7AC7SOFTWARELEU A:152 , TRP A:164 , ARG A:188BINDING SITE FOR RESIDUE GOL A 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:203 -Pro A:204

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3EXM)

(-) 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:210
 aligned with Q9FBN7_STRCO | Q9FBN7 from UniProtKB/TrEMBL  Length:236

    Alignment length:210
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232
         Q9FBN7_STRCO    23 GHWAPGSHILWRYRENGGPHVHIARPVTVVRDDADLLAVWLAPGTECVKPVLADGTPVHLEPLATRYTKPRTVQRDQWFGTGVLKLARPGEAWSVWLFWDPGWRFKNWYVNLERPLTRWEGGVDSEDHFLDISVHPDRTWHWRDEDEFAQALRDGLMDPASAGRVRRAGRSAVAEIRAWGSPFADGWEHWRPDPAWPVPSLPGDWDRTPA 232
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3exmA01 A:23-217 FomD barrel-like domain                                                                                                                                                           --------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeeee......eeeeeeeeeeeee..eeeeee....eeeeeee....hhhhhhhhhhh...eeeeeee.....eeeee.....eeeeeeee...eeeeeeeeee...eee..eeee.eeeeeeee.....eeeehhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3exm A  23 GHWAPGSHILWRYRENGGPHVHIARPVTVVRDDADLLAVWLAPGTECVKPVLADGTPVHLEPLATRYTKPRTVQRDQWFGTGVLKLARPGEAWSVWLFWDPGWRFKNWYVNLERPLTRWEGGVDSEDHFLDISVHPDRTWHWRDEDEFAQALRDGLMDPASAGRVRRAGRSAVAEIRAWGSPFADGWEHWRPDPAWPVPSLPGDWDRTPA 232
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232
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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 3EXM)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9FBN7_STRCO | Q9FBN7)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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        Q9FBN7_STRCO | Q9FBN7: 3cbt

(-) Related Entries Specified in the PDB File

3cbt CRYSTAL STRUCTURE OF SC4828, A UNIQUE PHOSPHATASE FROM STREPTOMYCES COELICOLOR RELATED ID: APC7349 RELATED DB: TARGETDB