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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE OLIGO-NUCLEOTIDE BINDING PROTEIN (ATU3699, AGR_L_2275) FROM AGROBACTERIUM TUMEFACIENS STR. C58 AT 1.60 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  24 May 04  (Deposition) - 08 Jun 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Hypothetical Protein (Atu3699) From Agrobacterium Tumefaciens At 1. 60 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN ATU3699
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ATU3699
    Organism Scientific: AGROBACTERIUM TUMEFACIENS STR. C58
    Organism Taxid: 176299
    Strain: C58 / ATCC 33970

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:33 , VAL A:34 , GLY B:104 , SER B:105 , VAL B:106 , HOH B:182 , HOH B:186 , HOH B:382BINDING SITE FOR RESIDUE SO4 B 170
2AC2SOFTWAREGLY A:104 , SER A:105 , VAL A:106 , HOH A:187 , HOH A:189 , HOH A:322 , PHE B:32 , THR B:33 , VAL B:34BINDING SITE FOR RESIDUE SO4 A 170
3AC3SOFTWARELYS A:50 , VAL A:72 , VAL B:34 , GLN B:38 , ARG B:41 , ASN B:69 , HOH B:224 , HOH B:296 , HOH B:320BINDING SITE FOR RESIDUE GOL B 171
4AC4SOFTWAREVAL A:34 , GLN A:38 , HOH A:206 , HOH A:253 , HOH A:285 , LYS B:50 , LEU B:52 , ALA B:70 , VAL B:71 , VAL B:72BINDING SITE FOR RESIDUE GOL B 172
5AC5SOFTWAREGLY B:46 , HIS B:48 , GLU B:67 , GLU B:68 , ASN B:69 , HOH B:356 , HOH B:364BINDING SITE FOR RESIDUE GOL B 173
6AC6SOFTWARETHR A:24 , THR A:25 , LYS A:26 , LEU A:43 , PRO A:45 , HOH A:180 , HOH A:181 , HOH A:216BINDING SITE FOR RESIDUE GOL A 171

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VKI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VKI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VKI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VKI)

(-) Exons   (0, 0)

(no "Exon" information available for 1VKI)

(-) 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:165
 aligned with A9CFJ8_AGRFC | A9CFJ8 from UniProtKB/TrEMBL  Length:169

    Alignment length:165
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164     
         A9CFJ8_AGRFC     5 SRKTATELFEFLDGLGISHTTKQHEPVFTVAESQSLRDLIPGGHTKNLFVKDKKDQYFVLTVEENAVVDLKSVHKTIGAASRVSFGRPEKMLEYLGVVPGSVTVFGAINDTARQVTFVLDSDLLENELVNGHPLSNDQTTTIASKDLIRFLEATGHAPLVLKVSE 169
               SCOP domains d1vkia_ A: Hypothetical protein Atu3699                                                                                                                               SCOP domains
               CATH domains 1vkiA00 A:5-169  [code=3.90.960.10, no name defined]                                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh...eeee.....hhhhhhhhhh....eeeeeeeee.....eeeeeee........hhhhhhh.....ee.hhhhhhhhhh......hhhhhhhh....eeeeee.hhhhh.eeee......eeeeeehhhhhhhhhhh....eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vki A   5 SRKTATELFEFLDGLGISHTTKQHEPVFTVAESQSLRDLIPGGHTKNLFVKDKKDQYFVLTVEENAVVDLKSVHKTIGAASRVSFGRPEKMLEYLGVVPGSVTVFGAINDTARQVTFVLDSDLLENELVNGHPLSNDQTTTIASKDLIRFLEATGHAPLVLKVSE 169
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164     


Chain B from PDB  Type:PROTEIN  Length:166
 aligned with A9CFJ8_AGRFC | A9CFJ8 from UniProtKB/TrEMBL  Length:169

    Alignment length:166
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163      
         A9CFJ8_AGRFC     4 NSRKTATELFEFLDGLGISHTTKQHEPVFTVAESQSLRDLIPGGHTKNLFVKDKKDQYFVLTVEENAVVDLKSVHKTIGAASRVSFGRPEKMLEYLGVVPGSVTVFGAINDTARQVTFVLDSDLLENELVNGHPLSNDQTTTIASKDLIRFLEATGHAPLVLKVSE 169
               SCOP domains d1vkib_ B: Hypothetical protein Atu3699                                                                                                                                SCOP domains
               CATH domains 1vkiB00 B:4-169  [code=3.90.960.10, no name defined]                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh...eeee.....hhhhhhhhhhh...eeeeeeeee.....eeeeeee........hhhhhhh.....ee.hhhhhhhhhh......hhhhhhhh....eeeeee.hhhhh.eeee......eeeeeehhhhhhhhhhh....eee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vki B   4 NSRKTATELFEFLDGLGISHTTKQHEPVFTVAESQSLRDLIPGGHTKNLFVKDKKDQYFVLTVEENAVVDLKSVHKTIGAASRVSFGRPEKMLEYLGVVPGSVTVFGAINDTARQVTFVLDSDLLENELVNGHPLSNDQTTTIASKDLIRFLEATGHAPLVLKVSE 169
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1VKI)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A9CFJ8_AGRFC | A9CFJ8)
molecular function
    GO:0002161    aminoacyl-tRNA editing activity    The hydrolysis of an incorrectly aminoacylated tRNA.
biological process
    GO:0006450    regulation of translational fidelity    Any process that modulates the ability of the translational apparatus to interpret the genetic code.

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