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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BSTDEAD N-TERMINAL DOMAIN
 
Authors :  A. B. Carmel, B. W. Matthews
Date :  17 Jul 03  (Deposition) - 14 Oct 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Dead Protein, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. B. Carmel, B. W. Matthews
Crystal Structure Of The Bstdead N-Terminal Domain: A Novel Dead Protein From Bacillus Stearothermophilus
Rna V. 10 66 2004
PubMed-ID: 14681586  |  Reference-DOI: 10.1261/RNA.5134304
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BSTDEAD
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)GOLD
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422

 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  (1, 16)

Asymmetric Unit (1, 16)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1Q0U)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q0U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Q0U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q0U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q0U)

(-) Exons   (0, 0)

(no "Exon" information available for 1Q0U)

(-) 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:209
 aligned with P83699_GEOSE | P83699 from UniProtKB/TrEMBL  Length:219

    Alignment length:209
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203         
         P83699_GEOSE     4 TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESXVGQSQTGTGKTHAYLLPIXEKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRXIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLXLDXGFITDVDQIAARXPKDLQXLVFSATIPEKLKPFLKKYXENPTFVHVL 212
               SCOP domains d1q0ua_ A: Probable DEAD box RNA helicase YqfR                                                                                                                                                                    SCOP domains
               CATH domains 1q0uA00 A:4-212 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhh.........eeeehhhhhhhhhhh...hhhhh.eeee.hhhhhhhh.hhhhhhhhhhh.....eeeeee...hhhhhhhhhhhh...eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q0u A   4 TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESmVGQSQTGTGKTHAYLLPImEKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRmIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLmLDmGFITDVDQIAARmPKDLQmLVFSATIPEKLKPFLKKYmENPTFVHVL 212
                                    13        23        33        43|       53        63        73        83        93       103|      113       123       133       143       153       163 |     173    |  183|      193       203         
                                                                   44-MSE             63-MSE                                  104-MSE                                                   162-MSE         178-MSE |                203-MSE     
                                                                                                                                                                                           165-MSE            184-MSE                        


Chain B from PDB  Type:PROTEIN  Length:210
 aligned with P83699_GEOSE | P83699 from UniProtKB/TrEMBL  Length:219

    Alignment length:210
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
         P83699_GEOSE     2 AETQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESXVGQSQTGTGKTHAYLLPIXEKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRXIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLXLDXGFITDVDQIAARXPKDLQXLVFSATIPEKLKPFLKKYXENPTFVHV 211
               SCOP domains d1q0ub_ B: Probable DEAD box RNA helicase YqfR                                                                                                                                                                     SCOP domains
               CATH domains 1q0uB00 B:2-211 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                               CATH domains
           Pfam domains (1) --------------------------DEAD-1q0uB01 B:28-198                                                                                                                                                      ------------- Pfam domains (1)
           Pfam domains (2) --------------------------DEAD-1q0uB02 B:28-198                                                                                                                                                      ------------- Pfam domains (2)
         Sec.struct. author ..hhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhh.......eeeehhhhhhhhhhh.........eeee.hhhhhhhh.hhhhhhhhhhh.....eeeeee...hhhhhhhhhhhh...eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1q0u B   2 AETQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESmVGQSQTGTGKTHAYLLPImEKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRmIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLmLDmGFITDVDQIAARmPKDLQmLVFSATIPEKLKPFLKKYmENPTFVHV 211
                                    11        21        31        41  |     51        61 |      71        81        91       101  |    111       121       131       141       151       161|  |   171      |181  |    191       201 |     211
                                                                     44-MSE             63-MSE                                  104-MSE                                                   162-MSE         178-MSE |                203-MSE    
                                                                                                                                                                                             165-MSE            184-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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (P83699_GEOSE | P83699)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.

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