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(-) Description

Title :  CRYSTAL STRUCTURE OF ARSENICAL RESISTANCE OPERON TRANS-ACTING REPRESSOR FROM BACTEROIDES VULGATUS ATCC 8482
 
Authors :  Y. Kim, C. Tesar, B. Feldmann, A. Joachimiak, Midwest Center For Str Genomics (Mcsg)
Date :  24 Nov 09  (Deposition) - 08 Dec 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (4x)
Biol. Unit 2:  A,B,C,D  (1x)
Keywords :  Alpha-Beta-Alpha Sandwich, Helix-Turn-Helix, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, C. Tesar, B. Feldmann, A. Joachimiak
Crystal Structure Of Arsenical Resistance Operon Trans-Acting Repressor From Bacteroides Vulgatus Atcc 8482
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ARSENICAL RESISTANCE OPERON TRANS-ACTING REPRESSOR
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21 MAGIC
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-103
    Gene: BVU_4185
    Organism Scientific: BACTEROIDES VULGATUS
    Organism Taxid: 435590
    Strain: ATCC 8482

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (4x): ABCD
Biological Unit 2 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 22)

Asymmetric Unit (4, 22)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2CA1Ligand/IonCALCIUM ION
3GOL3Ligand/IonGLYCEROL
4MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 84)
No.NameCountTypeFull Name
1ACY8Ligand/IonACETIC ACID
2CA-1Ligand/IonCALCIUM ION
3GOL12Ligand/IonGLYCEROL
4MSE64Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (3, 21)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2CA-1Ligand/IonCALCIUM ION
3GOL3Ligand/IonGLYCEROL
4MSE16Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:10 , CYS A:12 , HOH A:392 , ALA C:10 , ARG C:49BINDING SITE FOR RESIDUE GOL A 112
2AC2SOFTWARECYS B:12 , GLY B:16 , CYS B:18 , ARG D:49 , GOL D:112BINDING SITE FOR RESIDUE ACY B 111
3AC3SOFTWAREHOH A:114 , MSE C:11 , CYS C:12 , GLY C:16 , HOH C:285 , HOH C:486BINDING SITE FOR RESIDUE ACY C 111
4AC4SOFTWARESER A:-2 , GLY A:99 , HOH A:379 , SER C:85 , GLN C:86BINDING SITE FOR RESIDUE GOL C 113
5AC5SOFTWAREASP D:71 , GLN D:86 , HOH D:367BINDING SITE FOR RESIDUE CA D 111
6AC6SOFTWAREACY B:111 , ALA D:10 , ARG D:49BINDING SITE FOR RESIDUE GOL D 112

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:12 -C:12
2A:13 -A:18
3B:12 -D:12
4B:13 -B:18
5C:13 -C:18
6D:13 -D:18

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:73 -Pro A:74
2Leu B:73 -Pro B:74
3Leu C:73 -Pro C:74
4Leu D:73 -Pro D:74

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KTB)

(-) 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:106
 aligned with A6L7X2_BACV8 | A6L7X2 from UniProtKB/TrEMBL  Length:108

    Alignment length:106
                               1                                                                                                      
                               |     7        17        27        37        47        57        67        77        87        97      
         A6L7X2_BACV8     - ---MKKIEIFDPAMCCPTGLCGTNINPELMRIAVVIESLKKQGIIVTRHNLRDEPQVYVSNKTVNDFLQKHGADALPITLVDGEIAVSQTYPTTKQMSEWTGVNLD 103
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee..............hhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhh.hhhhh.eeee..eeee.....hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3ktb A  -2 SNAmKKIEIFDPAmCCPTGLCGTNINPELmRIAVVIESLKKQGIIVTRHNLRDEPQVYVSNKTVNDFLQKHGADALPITLVDGEIAVSQTYPTTKQmSEWTGVNLD 103
                               |     7   |    17        27        37        47        57        67        77        87      | 97      
                               |        11-MSE          27-MSE                                                             94-MSE     
                               1-MSE                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:102
 aligned with A6L7X2_BACV8 | A6L7X2 from UniProtKB/TrEMBL  Length:108

    Alignment length:102
                                    10        20        30        40        50        60        70        80        90       100  
         A6L7X2_BACV8     1 MKKIEIFDPAMCCPTGLCGTNINPELMRIAVVIESLKKQGIIVTRHNLRDEPQVYVSNKTVNDFLQKHGADALPITLVDGEIAVSQTYPTTKQMSEWTGVNL 102
               SCOP domains ------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee..............hhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhhhhhhhhhhh.eeee..eeeee....hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 3ktb B   1 mKKIEIFDPAmCCPTGLCGTNINPELmRIAVVIESLKKQGIIVTRHNLRDEPQVYVSNKTVNDFLQKHGADALPITLVDGEIAVSQTYPTTKQmSEWTGVNL 102
                            |       10|       20      | 30        40        50        60        70        80        90   |   100  
                            1-MSE    11-MSE          27-MSE                                                             94-MSE    


Chain C from PDB  Type:PROTEIN  Length:104
 aligned with A6L7X2_BACV8 | A6L7X2 from UniProtKB/TrEMBL  Length:108

    Alignment length:104
                             1                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99    
         A6L7X2_BACV8     - -MKKIEIFDPAMCCPTGLCGTNINPELMRIAVVIESLKKQGIIVTRHNLRDEPQVYVSNKTVNDFLQKHGADALPITLVDGEIAVSQTYPTTKQMSEWTGVNLD 103
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..............hhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhhhhh.eeee..eeeee....hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 3ktb C   0 AmKKIEIFDPAmCCPTGLCGTNINPELmRIAVVIESLKKQGIIVTRHNLRDEPQVYVSNKTVNDFLQKHGADALPITLVDGEIAVSQTYPTTKQmSEWTGVNLD 103
                             |       9 |      19       |29        39        49        59        69        79        89    |   99    
                             1-MSE    11-MSE          27-MSE                                                             94-MSE     


Chain D from PDB  Type:PROTEIN  Length:104
 aligned with A6L7X2_BACV8 | A6L7X2 from UniProtKB/TrEMBL  Length:108

    Alignment length:104
                             1                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99    
         A6L7X2_BACV8     - -MKKIEIFDPAMCCPTGLCGTNINPELMRIAVVIESLKKQGIIVTRHNLRDEPQVYVSNKTVNDFLQKHGADALPITLVDGEIAVSQTYPTTKQMSEWTGVNLD 103
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..............hhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhhhhh.eeee..eeeee....hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 3ktb D   0 AmKKIEIFDPAmCCPTGLCGTNINPELmRIAVVIESLKKQGIIVTRHNLRDEPQVYVSNKTVNDFLQKHGADALPITLVDGEIAVSQTYPTTKQmSEWTGVNLD 103
                             |       9 |      19       |29        39        49        59        69        79        89    |   99    
                             1-MSE    11-MSE          27-MSE                                                             94-MSE
   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  (0, 0)

(no "SCOP Domain" information available for 3KTB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KTB)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (A6L7X2_BACV8 | A6L7X2)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0046685    response to arsenic-containing substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an arsenic stimulus from compounds containing arsenic, including arsenates, arsenites, and arsenides.

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