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(-) Description

Title :  CRYSTAL STRUCTURE OF A PROBABLE RNA-BINDING PROTEIN FROM CLOSTRIDIUM SYMBIOSUM ATCC 14940
 
Authors :  K. Tan, L. Keigher, R. Jedrzejczak, G. Babnigg, A. Joachimiak, Midwest For Structural Genomics (Mcsg)
Date :  11 Mar 09  (Deposition) - 31 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Keywords :  Apc21302, Rna-Binding Protein, Clostridium Symbiosum Atcc 14940, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, L. Keigher, R. Jedrzejczak, G. Babnigg, A. Joachimiak
The Crystal Structure Of A Probable Rna-Binding Protein Fro Clostridium Symbiosum Atcc 14940
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROBABLE RNA-BINDING PROTEIN
    Atcc: 14940
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19
    Expression System Strain: PRK1037
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: CLOSTRIDIUM SYMBIOSUM ATCC 14940
    Organism Taxid: 411472

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): AB 
Biological Unit 2 (2x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 19)

Asymmetric Unit (1, 19)
No.NameCountTypeFull Name
1MSE19Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 13)
No.NameCountTypeFull Name
1MSE13Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3GKU)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:196 -Pro A:197
2Glu B:196 -Pro B:197

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3GKU)

(-) 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:206
 aligned with D0VX24_CLOSY | D0VX24 from UniProtKB/TrEMBL  Length:225

    Alignment length:208
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203        
         D0VX24_CLOSY     4 MDMVTVTAKTVEEAVTKALIELQTTSDKLTYEIVEKGSAGFLGIGSKPAIIRAKRKETLQDKAIEFLEQVFDAMNMAVDISVEYNETEKEMNVNLKGDDMGILIGKRGQTLDSLQYLVSLVVNKSSSDYIRVKLDTENYRERRKETLETLAKNIAYKVKRTKRSVSLEPMNPYERRIIHAALQNDKYVVTRSDGEEPFRHVIISLKRE 211
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -3gkuA01 A:2-56                                         3gkuA02 A:57-137 a probable RNA-binding protein from clostridium symbiosum       3gkuA03 A:138-208  [code=3.30.1370.50, no name defined]                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.hhhhhhhhhhhhhh.hhh.eeeeeee......--.....eeeeeee..hhhhhhhhhhhhhhhhh....eeeeeee....eeeeeeehhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhhhhhhhhhh..ee....hhhhhhhhhhhh.....eeeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gku A   1 mDmVTVTAKTVEEAVTKALIELQTTSDKLTYEIVEKGSAGF--IGSKPAIIRAKRKETLQDKAIEFLEQVFDAmNmAVDISVEYNETEKEmNVNLKGDDmGILIGKRGQTLDSLQYLVSLVVNKSSSDYIRVKLDTENYRERRKETLETLAKNIAYKVKRTKRSVSLEPmNPYERRIIHAALQNDKYVVTRSDGEEPFRHVIISLKRE 208
                            | |     10        20        30        40|  |    50        60        70   | |  80        90|      100       110       120       130       140       150       160       170       180       190       200        
                            | |                                    41 44                            74-MSE           91-MSE  100-MSE                                                               170-MSE                                  
                            1-MSE                                                                     76-MSE                                                                                                                                
                              3-MSE                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:193
 aligned with D0VX24_CLOSY | D0VX24 from UniProtKB/TrEMBL  Length:225

    Alignment length:205
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204     
         D0VX24_CLOSY     5 DMVTVTAKTVEEAVTKALIELQTTSDKLTYEIVEKGSAGFLGIGSKPAIIRAKRKETLQDKAIEFLEQVFDAMNMAVDISVEYNETEKEMNVNLKGDDMGILIGKRGQTLDSLQYLVSLVVNKSSSDYIRVKLDTENYRERRKETLETLAKNIAYKVKRTKRSVSLEPMNPYERRIIHAALQNDKYVVTRSDGEEPFRHVIISLK 209
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3gkuB01 B:2-56                                         3gkuB02 B:57-137 a probable RNA-binding protein from clostridium symbiosum       3gkuB03 B:138-206  [code=3.30.1370.50, no name defined]               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...hhhhhhhhhhhh..hhh.eeee..------------...eeeeee..hhhhhhhhhhhhhhhhh......eeeee....eeeeee.hhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhh.....eeeeee......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gku B   2 DmVTVTAKTVEEAVTKALIELQTTSDKLTYEIV------------KPAIIRAKRKETLQDKAIEFLEQVFDAmNmAVDISVEYNETEKEmNVNLKGDDmGILIGKRGQTLDSLQYLVSLVVNKSSSDYIRVKLDTENYRERRKETLETLAKNIAYKVKRTKRSVSLEPmNPYERRIIHAALQNDKYVVTRSDGEEPFRHVIISLK 206
                             |      11        21        31  |      -     |  51        61        71  | |   81        91       101       111       121       131       141       151       161       171       181       191       201     
                             3-MSE                         34           47                         74-MSE           91-MSE  100-MSE                                                               170-MSE                                
                                                                                                     76-MSE                                                                                                                              


Chain C from PDB  Type:PROTEIN  Length:134
 aligned with D0VX24_CLOSY | D0VX24 from UniProtKB/TrEMBL  Length:225

    Alignment length:145
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143     
         D0VX24_CLOSY     4 MDMVTVTAKTVEEAVTKALIELQTTSDKLTYEIVEKGSAGFLGIGSKPAIIRAKRKETLQDKAIEFLEQVFDAMNMAVDISVEYNETEKEMNVNLKGDDMGILIGKRGQTLDSLQYLVSLVVNKSSSDYIRVKLDTENYRERRKE 148
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -3gkuC01 C:2-56                                         3gkuC02 C:57-145 a probable RNA-binding protein from clostridium symbiosum                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhh........eeeeee.-----------...eeeeee..hhhhhhhhhhhhhhhh......eeeeee....eeeeee....hhhhhh..hhhhhhhhhhhhhhhhhh.....eeeee.hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gku C   1 mDmVTVTAKTVEEAVTKALIELQTTSDKLTYEIVE-----------KPAIIRAKRKETLQDKAIEFLEQVFDAmNmAVDISVEYNETEKEmNVNLKGDDmGILIGKRGQTLDSLQYLVSLVVNKSSSDYIRVKLDTENYRERRKE 145
                            | |     10        20        30    |    -      | 50        60        70   | |  80        90|      100       110       120       130       140     
                            1-MSE                            35          47                         74-MSE           91-MSE  100-MSE                                         
                              3-MSE                                                                   76-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 3GKU)

(-) CATH Domains  (3, 8)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (D0VX24_CLOSY | D0VX24)
molecular function
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.

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  Cis Peptide Bonds
    Glu A:196 - Pro A:197   [ RasMol ]  
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