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(-) Description

Title :  CRYSTAL STRUCTURE OF MTHSBDS, THE HOMOLOGUE OF THE SHWACHMAN-BODIAN-DIAMOND SYNDROME PROTEIN IN THE EURIARCHAEON METHANOTHERMOBACTER THERMAUTOTROPHICUS
 
Authors :  C. L. Ng, M. N. Isupov, A. A. Lebedev, M. Ortiz-Lombardia, A. A. Antson
Date :  02 Mar 09  (Deposition) - 02 Jun 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Shwachman-Bodian-Diamond Syndrome Protein, Ribosome Binding, Conformational Flexibility, Rna-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. L. Ng, D. G. Waterman, E. V. Koonin, A. D. Walters, J. P. Chong, M. N. Isupov, A. A. Lebedev, D. H. Bunka, P. G. Stockley, M. Ortiz-Lombardia, A. A. Antson
Conformational Flexibility And Molecular Interactions Of An Archaeal Homologue Of The Shwachman-Bodian-Diamond Syndrome Protein.
Bmc Struct. Biol. V. 9 32 2009
PubMed-ID: 19454024  |  Reference-DOI: 10.1186/1472-6807-9-32

(-) Compounds

Molecule 1 - RIBOSOME MATURATION PROTEIN SDO1 HOMOLOG
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PYCL02
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Organism Scientific: METHANOTHERMOBACTER THERMAUTOTROPHICUS
    Organism Taxid: 187420
    Strain: DELTA H
    Synonym: MTHSBDS

 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, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL6Ligand/IonGLYCEROL
3SO43Ligand/IonSULFATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL4Ligand/IonGLYCEROL
3SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3SO43Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA B:168 , LEU B:230 , LYS B:232 , HOH B:2172 , HOH B:2173 , HOH B:2174 , HOH B:2175BINDING SITE FOR RESIDUE GOL B1233
02AC2SOFTWAREVAL A:167 , GLN A:211 , PHE A:214 , THR A:228 , ARG A:229 , HOH A:2213BINDING SITE FOR RESIDUE GOL A1233
03AC3SOFTWARELYS B:164 , GLY B:187 , LYS B:188 , GLU B:205 , PRO B:207BINDING SITE FOR RESIDUE GOL B1234
04AC4SOFTWAREHOH A:2227BINDING SITE FOR RESIDUE GOL A1234
05AC5SOFTWAREALA A:53 , GLU A:192 , HOH A:2073 , HOH A:2201 , HOH A:2203BINDING SITE FOR RESIDUE GOL A1235
06AC6SOFTWAREALA A:176 , GLY A:177 , TRP A:194 , HOH A:2203BINDING SITE FOR RESIDUE GOL A1236
07AC7SOFTWAREARG A:65 , HOH A:2082 , GLN B:195 , ARG B:229 , HOH B:2181 , HOH B:2182 , HOH B:2183BINDING SITE FOR RESIDUE SO4 B1238
08AC8SOFTWARELYS B:103 , ASN B:106 , ARG B:110 , HOH B:2176 , HOH B:2177BINDING SITE FOR RESIDUE SO4 B1235
09AC9SOFTWAREARG B:11 , GLN B:87 , HOH B:2178 , HOH B:2179BINDING SITE FOR RESIDUE SO4 B1236
10BC1SOFTWAREILE B:160 , LYS B:161BINDING SITE FOR RESIDUE CL B1237

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WBM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WBM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WBM)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UPF0023PS01267 Uncharacterized protein family UPF0023 signature.SDO1_METTH37-56
 		  2A:37-56
B:38-56
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UPF0023PS01267 Uncharacterized protein family UPF0023 signature.SDO1_METTH37-56
 		  1A:37-56
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UPF0023PS01267 Uncharacterized protein family UPF0023 signature.SDO1_METTH37-56
 		  1-
B:38-56

(-) Exons   (0, 0)

(no "Exon" information available for 2WBM)

(-) 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:234
 aligned with SDO1_METTH | O26781 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:234
                              1                                                                                                                                                                                                                                       
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228    
           SDO1_METTH     - --MVSLEDAVIARLESHGERFEVLVDPDLAAEFRREDSDVSVEDVLAVQEVFRDARKGDKASEEAMRKVFETADPLEVTPVILRRGTIQLTAEQRRQMIEDKRLKIINKIAREAINPQNGLPHPPKRIEKAMEEARVHVDPFKTVDEQVNIVLKAIRTKIPIKFEKVRVAIKIPGERAGSAYGVISNFGKITNEEWQNDGSWIAVVEIPGGLQDSFYQKLSELTGGNVETRLIK 232
               SCOP domains d2wbma1 A:-1-87 automated matches                                                        d2wbma2 A:88-162 automated matches                                         d2wbma3 A:163-232 automated matches                                    SCOP domains
               CATH domains --------2wbmA01 A:7-87  [code=3.30.1250.10, no name defined]                             ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeeeee..eeeeeeehhhhhhhhhh.....hhhhhh.....eee....ee.hhhhhhhhhh..hhhhhhhhhhhhheee.hhhhhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhh........hhhhhhhhhhhhhh.....ee.eeeeeeeehhhhhhhhhhhhhhhheeeeeee.....eeeeeeee..hhhhhhhhhhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------UPF0023  PDB: A:37-5-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wbm A  -1 SHMVSLEDAVIARLESHGERFEVLVDPDLAAEFRREDSDVSVEDVLAVQEVFRDARKGDKASEEAMRKVFETADPLEVTPVILRRGTIQLTAEQRRQMIEDKRLKIINKIAREAINPQNGLPHPPKRIEKAMEEARVHVDPFKTVDEQVNIVLKAIRTKIPIKFEKVRVAIKIPGEMAGSAYGVISNFGKITNEEWQNDGSWIAVVEIPGGLQDSFYQKLSELTGGNVETRLIK 232
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228    


Chain B from PDB  Type:PROTEIN  Length:227
 aligned with SDO1_METTH | O26781 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:232
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230  
           SDO1_METTH     1 MVSLEDAVIARLESHGERFEVLVDPDLAAEFRREDSDVSVEDVLAVQEVFRDARKGDKASEEAMRKVFETADPLEVTPVILRRGTIQLTAEQRRQMIEDKRLKIINKIAREAINPQNGLPHPPKRIEKAMEEARVHVDPFKTVDEQVNIVLKAIRTKIPIKFEKVRVAIKIPGERAGSAYGVISNFGKITNEEWQNDGSWIAVVEIPGGLQDSFYQKLSELTGGNVETRLIK 232
               SCOP domains d2wbmb1 B:1-87 automated matches                                                       d2wbmb2 B:88-162 automated matches                                         d2wbmb3 B:163-232 automated matches                                    SCOP domains
               CATH domains ------2wbmB01 B:7-87  [code=3.30     .1250.10, no name defined]                        ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----SBDS-2wbmB03 B:5-96                                                                         --SBDS_C-2wbmB01 B:99-221                                                                                                    ----------- Pfam domains (1)
           Pfam domains (2) ----SBDS-2wbmB04 B:5-96                                                                         --SBDS_C-2wbmB02 B:99-221                                                                                                    ----------- Pfam domains (2)
         Sec.struct. author .......eeeeeee..eeeeeeehhhhhhhhh-----.hhhhhh.....eee....ee.hhhhhhhhhh..hhhhhhhhhhhhheee.hhhhhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhh........hhhhhhhhhhhhhh.....ee.eeeeeeeehhhhhhhhhhhhhhhheeeeeee.....eeeeeeee..hhhhhhhhhhhhhh...eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------UPF0023  PDB: B:38-5-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wbm B   1 MVSLEDAVIARLESHGERFEVLVDPDLAAEFR-----VSVEDVLAVQEVFRDARKGDKASEEAMRKVFETADPLEVTPVILRRGTIQLTAEQRRQMIEDKRLKIINKIAREAINPQNGLPHPPKRIEKAMEEARVHVDPFKTVDEQVNIVLKAIRTKIPIKFEKVRVAIKIPGEMAGSAYGVISNFGKITNEEWQNDGSWIAVVEIPGGLQDSFYQKLSELTGGNVETRLIK 232
                                    10        20        30 |     |40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230  
                                                          32    38
   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  (3, 6)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: EF-G_C (20)
(-)
Clan: no clan defined [family: SBDS] (6)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SDO1_METTH | O26781)
biological process
    GO:0042256    mature ribosome assembly    The aggregation, arrangement and bonding together of the large and small ribosomal subunits into a functional ribosome.
    GO:0042254    ribosome biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.

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