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(-) Description

Title :  THE CRYSTAL STRUCTURE OF A POSSIBLE TRANSCRIPTION REGULATOR PROTEIN FROM SINORHIZOBIUM MELILOTI 1021
 
Authors :  K. Tan, X. Xu, H. Cui, S. Chin, A. Savchenko, A. Edwards, A. Joachimiak, M Center For Structural Genomics (Mcsg)
Date :  11 May 10  (Deposition) - 02 Jun 10  (Release) - 02 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Str Uctural Genomics, Mcsg, Midwest Center For Structural Genomics, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, X. Xu, H. Cui, S. Chin, A. Savchenko, A. Edwards, A. Joachimiak
The Crystal Structure Of A Possible Transcription Regulator Protein From Sinorhizobium Meliloti 1021
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE TRANSCRIPTIONAL REGULATOR
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15TV LIC
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: R00429, SMC01092
    Organism Scientific: SINORHIZOBIUM MELILOTI
    Organism Taxid: 266834
    Strain: 1021

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 29)

Asymmetric Unit (2, 29)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MSE28Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 14)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 14)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE14Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO D:269 , PRO D:270 , ASN D:271BINDING SITE FOR RESIDUE CL D 299

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MZ1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MZ1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MZ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MZ1)

(-) Exons   (0, 0)

(no "Exon" information available for 3MZ1)

(-) 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:208
 aligned with Q92SG7_RHIME | Q92SG7 from UniProtKB/TrEMBL  Length:296

    Alignment length:212
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292  
         Q92SG7_RHIME    83 LPKGRLRVETASAFANLVIIPALPEFHKKYPDIQIDLGVSDRTIDYLAENVDCAIRAGTLTDQSLIARRITEMKFVACASRDFLERHPVPQHPSDLEKNCYVVGYFLPKTGQQMPFHFRRGNEEIEVSGRYTVAANESTTYLAAARAGLGVIQAPLFMVREDLRNGTMVPVLPDWQVEPMPIYLVYPPNRHLSSRLRVFADWVVKVMAQSQN 294
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeehhhhhhhhhhhhhhhhhhhh..eeeeeee....--.......eeeee........eeeeeeee.eeeeeehhhhhhh....hhhhhh....eeee....--....eeeee..eeeee...eeeee.hhhhhhhhhhh....eeeehhhhhhhhhh..eee.........eeeeeee......hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mz1 A  83 LPKGRLRVETASAFANLVIIPALPEFHKKYPDIQIDLGVSDRT--YLAENVDCAIRAGTLTDQSLIARRITEmKFVACASRDFLERHPVPQHPSDLEKNCYVVGYFLPK--QQmPFHFRRGNEEIEVSGRYTmAANESTTYLAAARAGLGVIQAPLFmVREDLRNGTmVPVLPDWQVEPmPIYLVYPPNRHLSSRLRVFADWVVKVmAQSQN 294
                                    92       102       112       122  |  | 132       142       152  |    162       172       182        |- | |   202       212  |    222       232       242       252       262       272       282      |292  
                                                                    125  |                        155-MSE                             191  | |                215-MSE                  240-MSE   250-MSE     262-MSE                    289-MSE 
                                                                       128                                                               194 |                                                                                                  
                                                                                                                                           196-MSE                                                                                              


Chain B from PDB  Type:PROTEIN  Length:212
 aligned with Q92SG7_RHIME | Q92SG7 from UniProtKB/TrEMBL  Length:296

    Alignment length:212
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292  
         Q92SG7_RHIME    83 LPKGRLRVETASAFANLVIIPALPEFHKKYPDIQIDLGVSDRTIDYLAENVDCAIRAGTLTDQSLIARRITEMKFVACASRDFLERHPVPQHPSDLEKNCYVVGYFLPKTGQQMPFHFRRGNEEIEVSGRYTVAANESTTYLAAARAGLGVIQAPLFMVREDLRNGTMVPVLPDWQVEPMPIYLVYPPNRHLSSRLRVFADWVVKVMAQSQN 294
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeehhhhhhhhhhhhhhhhhhhh..eeeeeee.............eeeee........eeeeeeee.eeeeeehhhhhhh....hhhhhh....eeee..........eeeee..eeeee...eeeee.hhhhhhhhhhh....eeeehhhhhhhhhh..eee.....ee..eeeeeee......hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mz1 B  83 LPKGRLRVETASAFANLVIIPALPEFHKKYPDIQIDLGVSDRTIDYLAENVDCAIRAGTLTDQSLIARRITEmKFVACASRDFLERHPVPQHPSDLEKNCYVVGYFLPKTGQQmPFHFRRGNEEIEVSGRYTmAANESTTYLAAARAGLGVIQAPLFmVREDLRNGTmVPVLPDWQVEPmPIYLVYPPNRHLSSRLRVFADWVVKVmAQSQN 294
                                    92       102       112       122       132       142       152  |    162       172       182       192   |   202       212  |    222       232       242       252       262       272       282      |292  
                                                                                                  155-MSE                                  196-MSE            215-MSE                  240-MSE   250-MSE     262-MSE                    289-MSE 


Chain C from PDB  Type:PROTEIN  Length:204
 aligned with Q92SG7_RHIME | Q92SG7 from UniProtKB/TrEMBL  Length:296

    Alignment length:213
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292   
         Q92SG7_RHIME    83 LPKGRLRVETASAFANLVIIPALPEFHKKYPDIQIDLGVSDRTIDYLAENVDCAIRAGTLTDQSLIARRITEMKFVACASRDFLERHPVPQHPSDLEKNCYVVGYFLPKTGQQMPFHFRRGNEEIEVSGRYTVAANESTTYLAAARAGLGVIQAPLFMVREDLRNGTMVPVLPDWQVEPMPIYLVYPPNRHLSSRLRVFADWVVKVMAQSQNG 295
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeehhhhhhhhhhhhhhhhhhhh..eeeeeee...---.......eeeee..----..eeeeeeee.eeeeeehhhhhhh......hhhhhh..eeee....--....eeeee..eeeee...eeeee.hhhhhhhhhhh....eeee...hhhhhhh..eee.....ee..eeeeeee......hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mz1 C  83 LPKGRLRVETASAFANLVIIPALPEFHKKYPDIQIDLGVSDR---YLAENVDCAIRAGT----SLIARRITEmKFVACASRDFLERHPVPQHPSDLEKNCYVVGYFLPK--QQmPFHFRRGNEEIEVSGRYTmAANESTTYLAAARAGLGVIQAPLFmVREDLRNGTmVPVLPDWQVEPmPIYLVYPPNRHLSSRLRVFADWVVKVmAQSQNG 295
                                    92       102       112       122 |   | 132        |-   |   152  |    162       172       182        |- | |   202       212  |    222       232       242       252       262       272       282      |292   
                                                                   124 128          141  146      155-MSE                             191  | |                215-MSE                  240-MSE   250-MSE     262-MSE                    289-MSE  
                                                                                                                                         194 |                                                                                                   
                                                                                                                                           196-MSE                                                                                               


Chain D from PDB  Type:PROTEIN  Length:212
 aligned with Q92SG7_RHIME | Q92SG7 from UniProtKB/TrEMBL  Length:296

    Alignment length:212
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292  
         Q92SG7_RHIME    83 LPKGRLRVETASAFANLVIIPALPEFHKKYPDIQIDLGVSDRTIDYLAENVDCAIRAGTLTDQSLIARRITEMKFVACASRDFLERHPVPQHPSDLEKNCYVVGYFLPKTGQQMPFHFRRGNEEIEVSGRYTVAANESTTYLAAARAGLGVIQAPLFMVREDLRNGTMVPVLPDWQVEPMPIYLVYPPNRHLSSRLRVFADWVVKVMAQSQN 294
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) LysR_substrate-3mz1D01 D:83-290                                                                                                                                                                                 ---- Pfam domains (1)
           Pfam domains (2) LysR_substrate-3mz1D02 D:83-290                                                                                                                                                                                 ---- Pfam domains (2)
           Pfam domains (3) LysR_substrate-3mz1D03 D:83-290                                                                                                                                                                                 ---- Pfam domains (3)
           Pfam domains (4) LysR_substrate-3mz1D04 D:83-290                                                                                                                                                                                 ---- Pfam domains (4)
         Sec.struct. author ...eeeeeeehhhhhhhhhhhhhhhhhhhh..eeeeeee.............eeeee........eeeeeeee.eeeeeehhhhhhh....hhhhhh....eeeeee....ee..eeeee..eeeee...eeeee.hhhhhhhhhhh....eeeehhhhhhhhhh..eee.........eeeeeeehhhhh.hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mz1 D  83 LPKGRLRVETASAFANLVIIPALPEFHKKYPDIQIDLGVSDRTIDYLAENVDCAIRAGTLTDQSLIARRITEmKFVACASRDFLERHPVPQHPSDLEKNCYVVGYFLPKTGQQmPFHFRRGNEEIEVSGRYTmAANESTTYLAAARAGLGVIQAPLFmVREDLRNGTmVPVLPDWQVEPmPIYLVYPPNRHLSSRLRVFADWVVKVmAQSQN 294
                                    92       102       112       122       132       142       152  |    162       172       182       192   |   202       212  |    222       232       242       252       262       272       282      |292  
                                                                                                  155-MSE                                  196-MSE            215-MSE                  240-MSE   250-MSE     262-MSE                    289-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 3MZ1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MZ1)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q92SG7_RHIME | Q92SG7)
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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