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(-) Description

Title :  THE CRYSTAL STRUCTURE OF A MARR FAMILY TRANSCRIPTIONAL REGULATOR FROM SILICIBACTER POMEROYI DSS.
 
Authors :  K. Tan, L. Volkart, L. Freeman, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  15 Aug 08  (Deposition) - 02 Sep 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Apc88769, Marr, Silicibacter Pomeroyi Dss, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Dna-Binding, Plasmid, Transcription, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, L. Volkart, L. Freeman, A. Joachimiak
The Crystal Structure Of A Marr Family Transcriptional Regulator From Silicibacter Pomeroyi Dss.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MARR FAMILY TRANSCRIPTIONAL REGULATOR
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21
    Expression System Vector Type: PLASMID
    Gene: SPOA0451
    Organism Scientific: SILICIBACTER POMEROYI
    Organism Taxid: 89184
    Strain: DSS

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3E6M)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3E6M)

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Phe A:12 -Pro A:13
2Phe C:12 -Pro C:13
3Phe D:12 -Pro D:13
4Phe E:12 -Pro E:13
5Phe F:12 -Pro F:13
6Phe G:12 -Pro G:13
7Phe H:12 -Pro H:13

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3E6M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3E6M)

(-) Exons   (0, 0)

(no "Exon" information available for 3E6M)

(-) 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:146
 aligned with Q5LLB9_RUEPO | Q5LLB9 from UniProtKB/TrEMBL  Length:158

    Alignment length:149
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147         
         Q5LLB9_RUEPO     8 PKPSFPYGSPGELNSFLPYLLTRITHIWSSELNQALASEKLPTPKLRLLSSLSAYGELTVGQLATLGVMEQSTTSRTVDQLVDEGLAARSISDADQRKRTVVLTRKGKKKLAEISPLINDFHAELVGNVDPDKLQTCIEVLGEILKGKT 156
               SCOP domains d3e6ma_ A: automated matches                                                                                                                          SCOP domains
               CATH domains 3e6mA00 A:8-156 'winged helix' repressor DNA binding domain                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhheeehhhhhhhh..hhhhhhhhhhhhhhh..eee..---.....eeeehhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e6m A   8 PKPSFPYGSPGELNSFLPYLLTRITHIWSSELNQALASEKLPTPKLRLLSSLSAYGELTVGQLATLGVmEQSTTSRTVDQLVDEGLAARSI---DQRKRTVVLTRKGKKKLAEISPLINDFHAELVGNVDPDKLQTCIEVLGEILKGKT 156
                                    17        27        37        47        57        67        77        87        97|   |  107       117       127       137       147         
                                                                                               76-MSE                98 102                                                      


Chain B from PDB  Type:PROTEIN  Length:147
 aligned with Q5LLB9_RUEPO | Q5LLB9 from UniProtKB/TrEMBL  Length:158

    Alignment length:149
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149         
         Q5LLB9_RUEPO    10 PSFPYGSPGELNSFLPYLLTRITHIWSSELNQALASEKLPTPKLRLLSSLSAYGELTVGQLATLGVMEQSTTSRTVDQLVDEGLAARSISDADQRKRTVVLTRKGKKKLAEISPLINDFHAELVGNVDPDKLQTCIEVLGEILKGKTDY 158
               SCOP domains d3e6mb_ B: automated matches                                                                                                                          SCOP domains
               CATH domains 3e6mB00 B:10-158 'winged helix' repressor DNA binding domain                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.eehhhhhhhh..hhhhhhhhhhhhhhh..eee....--....eeeehhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e6m B  10 PSFPYGSPGELNSFLPYLLTRITHIWSSELNQALASEKLPTPKLRLLSSLSAYGELTVGQLATLGVmEQSTTSRTVDQLVDEGLAARSISD--QRKRTVVLTRKGKKKLAEISPLINDFHAELVGNVDPDKLQTCIEVLGEILKGKTDY 158
                                    19        29        39        49        59        69      | 79        89        99|  |   109       119       129       139       149         
                                                                                             76-MSE                 100  |                                                       
                                                                                                                       103                                                       


Chain C from PDB  Type:PROTEIN  Length:146
 aligned with Q5LLB9_RUEPO | Q5LLB9 from UniProtKB/TrEMBL  Length:158

    Alignment length:149
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147         
         Q5LLB9_RUEPO     8 PKPSFPYGSPGELNSFLPYLLTRITHIWSSELNQALASEKLPTPKLRLLSSLSAYGELTVGQLATLGVMEQSTTSRTVDQLVDEGLAARSISDADQRKRTVVLTRKGKKKLAEISPLINDFHAELVGNVDPDKLQTCIEVLGEILKGKT 156
               SCOP domains d3e6mc_ C: automated matches                                                                                                                          SCOP domains
               CATH domains 3e6mC00 C:8-156 'winged helix' repressor DNA binding domain                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhheeehhhhhhhh..hhhhhhhhhhhhhhh..eeeeee.---.eeeeeehhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e6m C   8 PKPSFPYGSPGELNSFLPYLLTRITHIWSSELNQALASEKLPTPKLRLLSSLSAYGELTVGQLATLGVmEQSTTSRTVDQLVDEGLAARSISD---RKRTVVLTRKGKKKLAEISPLINDFHAELVGNVDPDKLQTCIEVLGEILKGKT 156
                                    17        27        37        47        57        67        77        87        97  |   |107       117       127       137       147         
                                                                                               76-MSE                 100 104                                                    


Chain D from PDB  Type:PROTEIN  Length:149
 aligned with Q5LLB9_RUEPO | Q5LLB9 from UniProtKB/TrEMBL  Length:158

    Alignment length:149
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149         
         Q5LLB9_RUEPO    10 PSFPYGSPGELNSFLPYLLTRITHIWSSELNQALASEKLPTPKLRLLSSLSAYGELTVGQLATLGVMEQSTTSRTVDQLVDEGLAARSISDADQRKRTVVLTRKGKKKLAEISPLINDFHAELVGNVDPDKLQTCIEVLGEILKGKTDY 158
               SCOP domains d3e6md_ D: automated matches                                                                                                                          SCOP domains
               CATH domains 3e6mD00 D:10-158 'winged helix' repressor DNA binding domain                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.eehhhhhhhh..hhhhhhhhhhhhhhh..eeeee.......eeeeehhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e6m D  10 PSFPYGSPGELNSFLPYLLTRITHIWSSELNQALASEKLPTPKLRLLSSLSAYGELTVGQLATLGVmEQSTTSRTVDQLVDEGLAARSISDADQRKRTVVLTRKGKKKLAEISPLINDFHAELVGNVDPDKLQTCIEVLGEILKGKTDY 158
                                    19        29        39        49        59        69      | 79        89        99       109       119       129       139       149         
                                                                                             76-MSE                                                                              


Chain E from PDB  Type:PROTEIN  Length:147
 aligned with Q5LLB9_RUEPO | Q5LLB9 from UniProtKB/TrEMBL  Length:158

    Alignment length:151
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157 
         Q5LLB9_RUEPO     8 PKPSFPYGSPGELNSFLPYLLTRITHIWSSELNQALASEKLPTPKLRLLSSLSAYGELTVGQLATLGVMEQSTTSRTVDQLVDEGLAARSISDADQRKRTVVLTRKGKKKLAEISPLINDFHAELVGNVDPDKLQTCIEVLGEILKGKTDY 158
               SCOP domains d3e6me_ E: automated matches                                                                                                                            SCOP domains
               CATH domains 3e6mE00 E:8-158 'winged helix' repressor DNA binding domain                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh.hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhh.eeeee.----..eeeeehhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e6m E   8 PKPSFPYGSPGELNSFLPYLLTRITHIWSSELNQALASEKLPTPKLRLLSSLSAYGELTVGQLATLGVmEQSTTSRTVDQLVDEGLAARSIS----RKRTVVLTRKGKKKLAEISPLINDFHAELVGNVDPDKLQTCIEVLGEILKGKTDY 158
                                    17        27        37        47        57        67        77        87        97 |    |107       117       127       137       147       157 
                                                                                               76-MSE                 99  104                                                      


Chain F from PDB  Type:PROTEIN  Length:146
 aligned with Q5LLB9_RUEPO | Q5LLB9 from UniProtKB/TrEMBL  Length:158

    Alignment length:149
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149         
         Q5LLB9_RUEPO    10 PSFPYGSPGELNSFLPYLLTRITHIWSSELNQALASEKLPTPKLRLLSSLSAYGELTVGQLATLGVMEQSTTSRTVDQLVDEGLAARSISDADQRKRTVVLTRKGKKKLAEISPLINDFHAELVGNVDPDKLQTCIEVLGEILKGKTDY 158
               SCOP domains d3e6mf_ F: automated matches                                                                                                                          SCOP domains
               CATH domains 3e6mF00 F:10-158 'winged helix' repressor DNA binding domain                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh.hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...eehhhhhhhhh..hhhhhhhhhhhhhhh..eee...---.....eeehhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e6m F  10 PSFPYGSPGELNSFLPYLLTRITHIWSSELNQALASEKLPTPKLRLLSSLSAYGELTVGQLATLGVmEQSTTSRTVDQLVDEGLAARSIS---QRKRTVVLTRKGKKKLAEISPLINDFHAELVGNVDPDKLQTCIEVLGEILKGKTDY 158
                                    19        29        39        49        59        69      | 79        89        99   |   109       119       129       139       149         
                                                                                             76-MSE                 99 103                                                       


Chain G from PDB  Type:PROTEIN  Length:148
 aligned with Q5LLB9_RUEPO | Q5LLB9 from UniProtKB/TrEMBL  Length:158

    Alignment length:151
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157 
         Q5LLB9_RUEPO     8 PKPSFPYGSPGELNSFLPYLLTRITHIWSSELNQALASEKLPTPKLRLLSSLSAYGELTVGQLATLGVMEQSTTSRTVDQLVDEGLAARSISDADQRKRTVVLTRKGKKKLAEISPLINDFHAELVGNVDPDKLQTCIEVLGEILKGKTDY 158
               SCOP domains d3e6mg_ G: automated matches                                                                                                                            SCOP domains
               CATH domains 3e6mG00 G:8-158 'winged helix' repressor DNA binding domain                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhh..eeeee.---...eeeeehhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e6m G   8 PKPSFPYGSPGELNSFLPYLLTRITHIWSSELNQALASEKLPTPKLRLLSSLSAYGELTVGQLATLGVmEQSTTSRTVDQLVDEGLAARSIS---QRKRTVVLTRKGKKKLAEISPLINDFHAELVGNVDPDKLQTCIEVLGEILKGKTDY 158
                                    17        27        37        47        57        67        77        87        97 |   | 107       117       127       137       147       157 
                                                                                               76-MSE                 99 103                                                       


Chain H from PDB  Type:PROTEIN  Length:147
 aligned with Q5LLB9_RUEPO | Q5LLB9 from UniProtKB/TrEMBL  Length:158

    Alignment length:149
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149         
         Q5LLB9_RUEPO    10 PSFPYGSPGELNSFLPYLLTRITHIWSSELNQALASEKLPTPKLRLLSSLSAYGELTVGQLATLGVMEQSTTSRTVDQLVDEGLAARSISDADQRKRTVVLTRKGKKKLAEISPLINDFHAELVGNVDPDKLQTCIEVLGEILKGKTDY 158
               SCOP domains d3e6mh_ H: automated matches                                                                                                                          SCOP domains
               CATH domains 3e6mH00 H:10-158 'winged helix' repressor DNA binding domain                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh.hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhheehhhhhhhhh..hhhhhhhhhhhhhhh..eeeee..--...eeeeehhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e6m H  10 PSFPYGSPGELNSFLPYLLTRITHIWSSELNQALASEKLPTPKLRLLSSLSAYGELTVGQLATLGVmEQSTTSRTVDQLVDEGLAARSISD--QRKRTVVLTRKGKKKLAEISPLINDFHAELVGNVDPDKLQTCIEVLGEILKGKTDY 158
                                    19        29        39        49        59        69      | 79        89        99|  |   109       119       129       139       149         
                                                                                             76-MSE                 100  |                                                       
                                                                                                                       103
   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  (2, 8)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E6M)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H   (Q5LLB9_RUEPO | Q5LLB9)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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