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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE METAL DEPENDENT PHOSPHOHYDROLASE (SAG1661) FROM STREPTOCOCCUS AGALACTIAE SEROGROUP V AT 1.85 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  05 Jan 07  (Deposition) - 16 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Conserved Hypothetical Protein Tigr00488 (Np_688652. 1) From Streptococcus Agalactiae 2603 At 1. 85 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN SAG1661
    Atcc: BAA-611
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NP_688652.1, SAG1661
    Organism Scientific: STREPTOCOCCUS AGALACTIAE SEROGROUP V
    Organism Taxid: 216466
    Strain: 2603 V/R
    Synonym: CONSERVED HYPOTHETICAL PROTEIN TIGR00488

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 17)

Asymmetric/Biological Unit (5, 17)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2FE4Ligand/IonFE (III) ION
3GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
4MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5MSE7Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:29 , HIS A:58 , ASP A:59 , ASP A:135 , FE A:302 , GDP A:400 , HOH A:406BINDING SITE FOR RESIDUE FE A 301
2AC2SOFTWAREASP A:59 , HIS A:91 , HIS A:117 , FE A:301 , GDP A:400 , HOH A:406BINDING SITE FOR RESIDUE FE A 302
3AC3SOFTWAREHIS B:29 , HIS B:58 , ASP B:59 , ASP B:135 , FE B:302 , GDP B:400 , HOH B:413BINDING SITE FOR RESIDUE FE B 301
4AC4SOFTWAREASP B:59 , HIS B:91 , HIS B:117 , FE B:301 , GDP B:400 , HOH B:413BINDING SITE FOR RESIDUE FE B 302
5AC5SOFTWAREGLY A:145 , VAL A:146 , GLU A:147BINDING SITE FOR RESIDUE CL A 303
6AC6SOFTWAREARG A:35 , HIS A:139 , HOH A:445BINDING SITE FOR RESIDUE CL A 305
7AC7SOFTWAREHIS A:29 , ASP A:59 , LYS A:62 , ASN A:88 , HIS A:91 , HIS A:117 , THR A:118 , ASP A:135 , ARG A:141 , LEU A:172 , PRO A:178 , ILE A:179 , TYR A:180 , THR A:183 , FE A:301 , FE A:302 , HOH A:406 , HOH A:412 , HOH A:414 , HOH A:444 , HOH A:462 , HOH A:515BINDING SITE FOR RESIDUE GDP A 400
8AC8SOFTWAREHIS B:29 , ASP B:59 , LYS B:62 , ASN B:88 , HIS B:91 , HIS B:117 , THR B:118 , ASP B:135 , ARG B:141 , THR B:168 , LEU B:172 , PRO B:178 , TYR B:180 , THR B:183 , FE B:301 , FE B:302 , HOH B:413 , HOH B:421 , HOH B:422 , HOH B:442 , HOH B:465 , HOH B:467 , HOH B:494 , HOH B:506 , HOH B:523BINDING SITE FOR RESIDUE GDP B 400
9AC9SOFTWARETHR B:2 , TYR B:3 , ARG B:11 , ILE B:38 , LYS B:48 , GLU B:49BINDING SITE FOR RESIDUE MES B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OGI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OGI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OGI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OGI)

(-) Exons   (0, 0)

(no "Exon" information available for 2OGI)

(-) 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:193
 aligned with Q8DY32_STRA5 | Q8DY32 from UniProtKB/TrEMBL  Length:195

    Alignment length:193
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192   
         Q8DY32_STRA5     3 YKDYTGLDRTELLSKVRHMMSDKRFNHVLGVERAAIELAERYGYDKEKAGLAALLHDYAKELSDDEFLRLIDKYQPDPDLKKWGNNIWHGLVGIYKIQEDLAIKDQDILAAIAKHTVGSAQMSTLDKIVYVADYIEHNRDFPGVEEARELAKVDLNKAVAYETARTVAFLASKAQPIYPKTIETYNAYIPYLD 195
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ogiA00 A:3-195 Hypothetical protein af1432                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh........hhhhhhhhhhhhhh......hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ogi A   3 YKDYTGLDRTELLSKVRHmmSDKRFNHVLGVERAAIELAERYGYDKEKAGLAALLHDYAKELSDDEFLRLIDKYQPDPDLKKWGNNIWHGLVGIYKIQEDLAIKDQDILAAIAKHTVGSAQmSTLDKIVYVADYIEHNRDFPGVEEARELAKVDLNKAVAYETARTVAFLASKAQPIYPKTIETYNAYIPYLD 195
                                    12        22        32        42        52        62        72        82        92       102       112       122 |     132       142       152       162       172       182       192   
                                             21-MSE                                                                                                124-MSE                                                                   
                                              22-MSE                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:195
 aligned with Q8DY32_STRA5 | Q8DY32 from UniProtKB/TrEMBL  Length:195

    Alignment length:195
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190     
         Q8DY32_STRA5     1 MTYKDYTGLDRTELLSKVRHMMSDKRFNHVLGVERAAIELAERYGYDKEKAGLAALLHDYAKELSDDEFLRLIDKYQPDPDLKKWGNNIWHGLVGIYKIQEDLAIKDQDILAAIAKHTVGSAQMSTLDKIVYVADYIEHNRDFPGVEEARELAKVDLNKAVAYETARTVAFLASKAQPIYPKTIETYNAYIPYLD 195
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -2ogiB00 B:2-195 Hypothetical protein af1432                                                                                                                                                        CATH domains
           Pfam domains (1) -------------------------HD-2ogiB01 B:26-140                                                                                                ------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------HD-2ogiB02 B:26-140                                                                                                ------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh........hhhhhhhhhhhhhh......hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ogi B   1 mTYKDYTGLDRTELLSKVRHmmSDKRFNHVLGVERAAIELAERYGYDKEKAGLAALLHDYAKELSDDEFLRLIDKYQPDPDLKKWGNNIWHGLVGIYKIQEDLAIKDQDILAAIAKHTVGSAQmSTLDKIVYVADYIEHNRDFPGVEEARELAKVDLNKAVAYETARTVAFLASKAQPIYPKTIETYNAYIPYLD 195
                            |       10        20||      30        40        50        60        70        80        90       100       110       120   |   130       140       150       160       170       180       190     
                            1-MSE              21-MSE                                                                                                124-MSE                                                                   
                                                22-MSE
   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 2OGI)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HD_PDEase (93)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8DY32_STRA5 | Q8DY32)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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