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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF BC1842 PROTEIN FROM BACILLUS CEREUS, A MEMBER OF THE RRF2 FAMILY OF PUTATIVE TRANSCRIPTION REGULATORS.
 
Authors :  J. Osipiuk, R. Wu, S. Moy, F. Collart, A. Joachimiak, Midwest Center F Structural Genomics (Mcsg)
Date :  19 Jan 05  (Deposition) - 01 Feb 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  A,B,C  (2x)
Biol. Unit 3:  A  (1x)
Biol. Unit 4:  B  (1x)
Biol. Unit 5:  C  (1x)
Keywords :  Structural Genomics, Rrf2 Family, Transcription Regulator, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Osipiuk, R. Wu, S. Moy, F. Collart, A. Joachimiak
X-Ray Crystal Structure Of Bc1842 Protein From Bacillus Cereus, A Member Of The Rrf2 Family Of Putative Transcription Regulators.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RRF2 FAMILY PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: BC1842
    Organism Scientific: BACILLUS CEREUS ATCC 14579
    Organism Taxid: 226900
    Strain: ATCC 14579 / DSM 31

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): ABC
Biological Unit 2 (2x): ABC
Biological Unit 3 (1x): A  
Biological Unit 4 (1x):  B 
Biological Unit 5 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 17)

Asymmetric Unit (2, 17)
No.NameCountTypeFull Name
1CL5Ligand/IonCHLORIDE ION
2MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 24)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE24Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (1, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 5 (1, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:25 , SER C:30BINDING SITE FOR RESIDUE CL B 201
2AC2SOFTWARESER B:30 , HOH B:210BINDING SITE FOR RESIDUE CL B 202
3AC3SOFTWARELYS C:21 , HIS C:73BINDING SITE FOR RESIDUE CL C 203
4AC4SOFTWARESER A:30 , ARG A:45BINDING SITE FOR RESIDUE CL A 204
5AC5SOFTWAREHOH B:207BINDING SITE FOR RESIDUE CL B 205

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly B:62 -Pro B:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YLF)

(-) 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:117
 aligned with Q81EX1_BACCR | Q81EX1 from UniProtKB/TrEMBL  Length:146

    Alignment length:138
                                    14        24        34        44        54        64        74        84        94       104       114       124       134        
         Q81EX1_BACCR     5 KISSRFSIAVHILSILKNNPSSLCTSDYMAESVNTNPVVIRKIMSYLKQAGFVYVNRGPGGAGLLKDLHEITLLDVYHAVNVVEEDKLFHIHEQPNPDCPIGANIQAVLEIILIQAQSAMEEVLRNITMGQLFETLQE 142
               SCOP domains d1ylfa1 A:5-142 Hypothetical protein BC1842                                                                                                SCOP domains
               CATH domains 1ylfA00 A:5-142 'winged helix' repressor DNA binding dom   ain                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..eee.---..eee..hhhhhhhhhhhhhhh.------------------hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ylf A   5 KISSRFSIAVHILSILKNNPSSLCTSDYmAESVNTNPVVIRKImSYLKQAGFVYVN---GGAGLLKDLHEITLLDVYHAVNV------------------IGANIQAVLEIILIQAQSAmEEVLRNITmGQLFETLQE 142
                                    14        24        34        44   |    54     |  64        74        84 |       -         -|      114       124       134        
                                                       33-MSE         48-MSE      60  64                    86                105                124-MSE  133-MSE     


Chain B from PDB  Type:PROTEIN  Length:118
 aligned with Q81EX1_BACCR | Q81EX1 from UniProtKB/TrEMBL  Length:146

    Alignment length:134
                                    16        26        36        46        56        66        76        86        96       106       116       126       136    
         Q81EX1_BACCR     7 SSRFSIAVHILSILKNNPSSLCTSDYMAESVNTNPVVIRKIMSYLKQAGFVYVNRGPGGAGLLKDLHEITLLDVYHAVNVVEEDKLFHIHEQPNPDCPIGANIQAVLEIILIQAQSAMEEVLRNITMGQLFETL 140
               SCOP domains d1ylfb_ B: automated matches                                                                                                           SCOP domains
               CATH domains 1ylfB00 B:7-140 'winged helix' repressor DNA binding domain                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh......hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee....eeee..hhhhhhhhhhhhhhh.----------------hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ylf B   7 SSRFSIAVHILSILKNNPSSLCTSDYmAESVNTNPVVIRKImSYLKQAGFVYVNRGPGGAGLLKDLHEITLLDVYHAVNV----------------CPIGANIQAVLEIILIQAQSAmEEVLRNITmGQLFETL 140
                                    16        26      | 36        46 |      56        66        76        86         -      |106       116       126      |136    
                                                     33-MSE         48-MSE                                86              103                  124-MSE  133-MSE   


Chain C from PDB  Type:PROTEIN  Length:119
 aligned with Q81EX1_BACCR | Q81EX1 from UniProtKB/TrEMBL  Length:146

    Alignment length:138
                                    15        25        35        45        55        65        75        85        95       105       115       125       135        
         Q81EX1_BACCR     6 ISSRFSIAVHILSILKNNPSSLCTSDYMAESVNTNPVVIRKIMSYLKQAGFVYVNRGPGGAGLLKDLHEITLLDVYHAVNVVEEDKLFHIHEQPNPDCPIGANIQAVLEIILIQAQSAMEEVLRNITMGQLFETLQEK 143
               SCOP domains d1ylfc_ C: automated matches                                                                                                               SCOP domains
               CATH domains 1ylfC00 C:6-143 'winged helix' repressor DNA binding domain                                                                                CATH domains
           Pfam domains (1) Rrf2-1ylfC01 C:6-84                                                            ----------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) Rrf2-1ylfC02 C:6-84                                                            ----------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) Rrf2-1ylfC03 C:6-84                                                            ----------------------------------------------------------- Pfam domains (3)
         Sec.struct. author .hhhhhhhhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhhhhh..eee......eee..hhhhhhhhhhhhhhh.-------------------.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ylf C   6 ISSRFSIAVHILSILKNNPSSLCTSDYmAESVNTNPVVIRKImSYLKQAGFVYVNRGPGGAGLLKDLHEITLLDVYHAVNV-------------------GANIQAVLEIILIQAQSAmEEVLRNITmGQLFETLQEK 143
                                    15        25       |35        45  |     55        65        75        85|        -         -|      115       125       135        
                                                      33-MSE         48-MSE                                86                 106               124-MSE  133-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  (2, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1YLF)

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 Related Entries

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(-) Related Entries Specified in the PDB File

1xd7 CRYSTAL STRUCTURE OF A PUTATIVE DNA BINDING PROTEIN RELATED ID: APC22838 RELATED DB: TARGETDB