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(-) Description

Title :  CRYSTAL STRUCTURE OF HYPOTHETICAL PROTEIN (GK2848) FROM GEOBACILLUS KAUSTOPHILUS
 
Authors :  P. P. Karthe, T. S. Kumarevel, S. Kuramitsu, S. Yokoyama, Riken Struct Genomics/Proteomics Initiative (Rsgi)
Date :  17 Jan 12  (Deposition) - 07 Mar 12  (Release) - 07 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. P. Karthe, T. S. Kumarevel, S. Kuramitsu, S. Yokoyama
Crystal Structure Of Hypothetical Protein (Gk2848) From Geobacillus Kaustophilus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL CONSERVED PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-HISTEV
    Expression System Strain: BL21(DE3)CODONPLUS-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GK2848
    Organism Scientific: GEOBACILLUS KAUSTOPHILUS
    Organism Taxid: 235909
    Strain: HTA426

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1ACY3Ligand/IonACETIC ACID
2MG3Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:147BINDING SITE FOR RESIDUE ACY A 201
2AC2SOFTWAREHIS A:64 , HIS A:86 , HIS C:81 , HOH C:326BINDING SITE FOR RESIDUE MG A 202
3AC3SOFTWARELEU B:131 , ARG B:141 , ASP B:147BINDING SITE FOR RESIDUE ACY B 201
4AC4SOFTWAREGLN A:58 , HIS A:81 , HOH A:320 , HIS B:64 , HIS B:86BINDING SITE FOR RESIDUE MG B 202
5AC5SOFTWAREASP C:147BINDING SITE FOR RESIDUE ACY C 201
6AC6SOFTWAREHIS B:81 , HOH B:316 , HIS C:64 , HIS C:86BINDING SITE FOR RESIDUE MG C 202

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Arg A:135 -Pro A:136
2Arg B:135 -Pro B:136
3Arg C:135 -Pro C:136

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3VNP)

(-) 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:171
 aligned with Q5KW03_GEOKA | Q5KW03 from UniProtKB/TrEMBL  Length:182

    Alignment length:171
                             1                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169 
         Q5KW03_GEOKA     - -MIYPYKGKTPQIAASAFIADYVTITGDVVIGEETSIWFNTVIRGDVAPTVIGNRVNIQDNSILHQSPNNPLIIEDGVTVGHQVILHSAIVRKNALIGMGSIILDRAEIGEGAFIGAGSLVPPGKKIPPNTLALGRPAKVVRELTEDDIREMERIRREYVEKGQYYKALQQ 170
               SCOP domains d3vnpa_ A: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.......ee....ee....eeeeeeee....ee....eeeeeeeeeee....ee....eee......eee....ee....eee..ee....ee....ee....ee....ee....ee....ee...eeee....eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vnp A   0 GMIYPYKGKTPQIAASAFIADYVTITGDVVIGEETSIWFNTVIRGDVAPTVIGNRVNIQDNSILHQSPNNPLIIEDGVTVGHQVILHSAIVRKNALIGMGSIILDRAEIGEGAFIGAGSLVPPGKKIPPNTLALGRPAKVVRELTEDDIREMERIRREYVEKGQYYKALQQ 170
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169 


Chain B from PDB  Type:PROTEIN  Length:171
 aligned with Q5KW03_GEOKA | Q5KW03 from UniProtKB/TrEMBL  Length:182

    Alignment length:171
                             1                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169 
         Q5KW03_GEOKA     - -MIYPYKGKTPQIAASAFIADYVTITGDVVIGEETSIWFNTVIRGDVAPTVIGNRVNIQDNSILHQSPNNPLIIEDGVTVGHQVILHSAIVRKNALIGMGSIILDRAEIGEGAFIGAGSLVPPGKKIPPNTLALGRPAKVVRELTEDDIREMERIRREYVEKGQYYKALQQ 170
               SCOP domains d3vnpb_ B: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.......ee....ee....eeeeeeee....ee....eeeeeeeeeee....ee....eee......eee....ee....eee..ee....ee....ee....ee....ee....ee....ee...eeee....eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vnp B   0 GMIYPYKGKTPQIAASAFIADYVTITGDVVIGEETSIWFNTVIRGDVAPTVIGNRVNIQDNSILHQSPNNPLIIEDGVTVGHQVILHSAIVRKNALIGMGSIILDRAEIGEGAFIGAGSLVPPGKKIPPNTLALGRPAKVVRELTEDDIREMERIRREYVEKGQYYKALQQ 170
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169 


Chain C from PDB  Type:PROTEIN  Length:171
 aligned with Q5KW03_GEOKA | Q5KW03 from UniProtKB/TrEMBL  Length:182

    Alignment length:171
                             1                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169 
         Q5KW03_GEOKA     - -MIYPYKGKTPQIAASAFIADYVTITGDVVIGEETSIWFNTVIRGDVAPTVIGNRVNIQDNSILHQSPNNPLIIEDGVTVGHQVILHSAIVRKNALIGMGSIILDRAEIGEGAFIGAGSLVPPGKKIPPNTLALGRPAKVVRELTEDDIREMERIRREYVEKGQYYKALQQ 170
               SCOP domains d3vnpc_ C: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.......ee....ee....eeeeeeee....ee....eeeeeeeeeee....ee....eee......eee....ee....eee..ee....ee....ee....ee....ee....ee....ee...eeee....eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vnp C   0 GMIYPYKGKTPQIAASAFIADYVTITGDVVIGEETSIWFNTVIRGDVAPTVIGNRVNIQDNSILHQSPNNPLIIEDGVTVGHQVILHSAIVRKNALIGMGSIILDRAEIGEGAFIGAGSLVPPGKKIPPNTLALGRPAKVVRELTEDDIREMERIRREYVEKGQYYKALQQ 170
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169
   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  (1, 3)

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

(-) CATH Domains  (0, 0 ; only for superseded entry 2EG0: 1,3)

(no "CATH Domain" information available for 3VNP, only for superseded entry 2EG0 replaced by 3VNP)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (Q5KW03_GEOKA | Q5KW03)
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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(-) Related Entries Specified in the PDB File

2eg0 RELATED ID: GKA001002848.1 RELATED DB: TARGETTRACK