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(-) Description

Title :  CRYSTAL STRUCTURE OF N-TERMINAL DOMAIN OF PUTATIVE ATP/GTP BINDING PROTEIN FROM CLOSTRIDIUM DIFFICILE 630
 
Authors :  B. Nocek, L. Bigelow, G. Cobb, A. Joachimiak, Midwest Center For Str Genomics (Mcsg)
Date :  05 Feb 09  (Deposition) - 10 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  N-Terminal Domain Of Atp/Gtp Binding Protein, Psi, Mcsg, Structural Genomics, Protein Structure Initiative, Midwest Center For Structural Genomics, Nucleotide Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Nocek, L. Bigelow, G. Cobb, A. Joachimiak
Crystal Structure Of N-Terminal Domain Of Putative Atp/Gtp Binding Protein From Clostridium Difficile 630
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE ATP/GTP BINDING PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-131
    Gene: CD1325
    Organism Scientific: CLOSTRIDIUM DIFFICILE
    Organism Taxid: 272563
    Strain: 630

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE6Mod. Amino AcidSELENOMETHIONINE
3PGE2Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE3Mod. Amino AcidSELENOMETHIONINE
3PGE1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2MSE3Mod. Amino AcidSELENOMETHIONINE
3PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:68BINDING SITE FOR RESIDUE PGE A 302
2AC2SOFTWAREARG A:21 , THR A:22 , GLU A:25 , PHE A:40 , HIS A:45 , CYS A:93 , ALA A:94 , ARG A:99 , HOH A:165BINDING SITE FOR RESIDUE GOL A 303
3AC3SOFTWARESER B:102BINDING SITE FOR RESIDUE PGE B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3G5J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3G5J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3G5J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3G5J)

(-) Exons   (0, 0)

(no "Exon" information available for 3G5J)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  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:130
 aligned with Q18BI8_PEPD6 | Q18BI8 from UniProtKB/TrEMBL  Length:352

    Alignment length:130
                                    11        21        31        41        51        61        71        81        91       101       111       121       131
         Q18BI8_PEPD6     2 SVIKIEKALKLDKVIFVDVRTEGEYEEDHILNAINMPLFKNNEHNEVGTIYKMQGKHEAIQKGFDYVSYKLKDIYLQAAELALNYDNIVIYCARGGMRSGSIVNLLSSLGVNVYQLEGGYKAYRNFVLEY 131
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3g5jA00 A:2-131 Oxidized Rhodanese, domain 1                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhh....eeeee..hhhhhhhh.....ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh....eee.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g5j A   2 SVIKIEKALKLDKVIFVDVRTEGEYEEDHILNAINmPLFKNNEHNEVGTIYKmQGKHEAIQKGFDYVSYKLKDIYLQAAELALNYDNIVIYCARGGmRSGSIVNLLSSLGVNVYQLEGGYKAYRNFVLEY 131
                                    11        21        31     |  41        51  |     61        71        81        91      |101       111       121       131
                                                              37-MSE           54-MSE                                      98-MSE                             


Chain B from PDB  Type:PROTEIN  Length:129
 aligned with Q18BI8_PEPD6 | Q18BI8 from UniProtKB/TrEMBL  Length:352

    Alignment length:129
                                    11        21        31        41        51        61        71        81        91       101       111       121         
         Q18BI8_PEPD6     2 SVIKIEKALKLDKVIFVDVRTEGEYEEDHILNAINMPLFKNNEHNEVGTIYKMQGKHEAIQKGFDYVSYKLKDIYLQAAELALNYDNIVIYCARGGMRSGSIVNLLSSLGVNVYQLEGGYKAYRNFVLE 130
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3g5jB00 B:2-130 Oxidized Rhodanese, domain 1                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhh...eeeee..hhhhhhhh.....ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh...eeee.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g5j B   2 SVIKIEKALKLDKVIFVDVRTEGEYEEDHILNAINmPLFKNNEHNEVGTIYKmQGKHEAIQKGFDYVSYKLKDIYLQAAELALNYDNIVIYCARGGmRSGSIVNLLSSLGVNVYQLEGGYKAYRNFVLE 130
                                    11        21        31     |  41        51  |     61        71        81        91      |101       111       121         
                                                              37-MSE           54-MSE                                      98-MSE
   Legend:   → Mismatch (orange background)
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  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 3G5J)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3G5J)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q18BI8_PEPD6 | Q18BI8)
molecular function
    GO:0043828    tRNA 2-selenouridine synthase activity    Catalysis of the reaction: 5-methylaminomethyl-2-thiouridine + selenophosphate = 5-methylaminomethyl-2-selenouridine + phosphate (at the wobble position in tRNA).
    GO:0016785    transferase activity, transferring selenium-containing groups    Catalysis of the transfer of a selenium-containing group from one compound (donor) to another (acceptor).
biological process
    GO:0070329    tRNA seleno-modification    The substitution of a selenium atom for a sulfur atom in a ribonucleotide in a tRNA molecule.

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