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(-) Description

Title :  THE STRUCTURE OF A PUTATIVE MODE FROM AGROBACTERIUM TUMEFACIENS.
 
Authors :  M. E. Cuff, E. Evdokimova, M. Kudritska, A. Edwards, A. Savchenko, A. Jo Midwest Center For Structural Genomics (Mcsg)
Date :  29 Sep 06  (Deposition) - 31 Oct 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Molybdenum-Binding, Transcriptional Repressor, Structural Genomics, Dna-Binding Protein, Agrobacterium Tumefaciens, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. E. Cuff, E. Evdokimova, M. Kudritska, A. Edwards, A. Savchenko, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
The Structure Of A Putative Mode From Agrobacterium Tumefaciens.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MOLYBDENUM-BINDING TRANSCRIPTIONAL REPRESSOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: P11
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MODE
    Organism Scientific: AGROBACTERIUM TUMEFACIENS STR.
    Organism Taxid: 176299
    Strain: C58
    Synonym: AGR_C_4647P

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 26)

Asymmetric/Biological Unit (3, 26)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2MSE12Mod. Amino AcidSELENOMETHIONINE
3SO48Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG B:13 , ARG B:21 , GLY B:23 , GLY B:25 , LYS B:26 , HOH B:363BINDING SITE FOR RESIDUE SO4 B 201
02AC2SOFTWAREARG A:21 , EDO A:302 , VAL B:11 , ARG B:13 , HIS B:24 , HOH B:321 , HOH B:353BINDING SITE FOR RESIDUE SO4 B 202
03AC3SOFTWAREARG A:13 , ARG A:21 , LEU A:22 , GLY A:23 , GLY A:25 , LYS A:26 , HOH A:323 , HOH A:341 , HOH A:345BINDING SITE FOR RESIDUE SO4 A 203
04AC4SOFTWAREARG A:13 , HIS A:24 , EDO A:302 , HOH A:309 , HOH A:335 , ARG B:21BINDING SITE FOR RESIDUE SO4 A 204
05AC5SOFTWARESER A:49 , ARG A:51 , ARG A:52 , HOH A:352BINDING SITE FOR RESIDUE SO4 A 205
06AC6SOFTWARECYS A:70 , SER A:71 , GLU A:107 , TRP A:111 , HOH A:315 , ARG B:93BINDING SITE FOR RESIDUE SO4 A 206
07AC7SOFTWARESER B:38 , ILE B:39 , SER B:40 , TYR B:50 , GLY B:79 , GLY B:80BINDING SITE FOR RESIDUE SO4 B 207
08AC8SOFTWAREARG A:51 , THR B:84 , VAL B:85 , HOH B:315BINDING SITE FOR RESIDUE SO4 B 208
09AC9SOFTWARESER B:49 , ARG B:51 , ARG B:52BINDING SITE FOR RESIDUE EDO B 301
10BC1SOFTWAREVAL A:11 , ARG A:13 , SO4 A:204 , VAL B:11 , ARG B:13 , SO4 B:202BINDING SITE FOR RESIDUE EDO A 302
11BC2SOFTWARESER A:40 , ARG A:44 , ARG B:65 , HOH B:348BINDING SITE FOR RESIDUE EDO B 303
12BC3SOFTWAREARG A:93 , HOH A:318BINDING SITE FOR RESIDUE EDO A 304
13BC4SOFTWARETRP B:111 , ASN B:115BINDING SITE FOR RESIDUE EDO B 305
14BC5SOFTWAREGLU B:113BINDING SITE FOR RESIDUE EDO B 306

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:17 -Pro A:18
2Pro B:17 -Pro B:18

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2IJL)

(-) Exons   (0, 0)

(no "Exon" information available for 2IJL)

(-) Sequences/Alignments

Asymmetric/Biological 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:110
 aligned with A9CHN1_AGRFC | A9CHN1 from UniProtKB/TrEMBL  Length:131

    Alignment length:116
                                    13        23        33        43        53        63        73        83        93       103       113      
         A9CHN1_AGRFC     4 KRLPLKPVLRIDFPPGERLGHGKVELMQLIAETGSISAAGRAMDMSYRRAWLLVDALNHMFRQPVICSQRGGKQGGGAALTVFGAELLERYRGMEERMNEALREDIDWLEANRNPQ 119
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ijlA00 A:4-119 'winged helix' repressor DNA binding domain                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee...eeehhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....eee..------.eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 2ijl A   4 KRLPLKPVLRIDFPPGERLGHGKVELmQLIAETGSISAAGRAmDmSYRRAWLLVDALNHmFRQPVICSQR------GAALTVFGAELLERYRGmEERmNEALREDIDWLEANRNPQ 119
                                    13        23      | 33        43  | |   53        63        73      | 83        93   |   103       113      
                                                     30-MSE          46-MSE           63-MSE    73     80               97-MSE                  
                                                                       48-MSE                                              101-MSE              


Chain B from PDB  Type:PROTEIN  Length:109
 aligned with A9CHN1_AGRFC | A9CHN1 from UniProtKB/TrEMBL  Length:131

    Alignment length:115
                                    14        24        34        44        54        64        74        84        94       104       114     
         A9CHN1_AGRFC     5 RLPLKPVLRIDFPPGERLGHGKVELMQLIAETGSISAAGRAMDMSYRRAWLLVDALNHMFRQPVICSQRGGKQGGGAALTVFGAELLERYRGMEERMNEALREDIDWLEANRNPQ 119
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ijlB00 B:5-119 'winged helix' repressor DNA binding domain                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee...eeehhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh....eee.------..eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2ijl B   5 RLPLKPVLRIDFPPGERLGHGKVELmQLIAETGSISAAGRAmDmSYRRAWLLVDALNHmFRQPVICSQ------GGAALTVFGAELLERYRGmEERmNEALREDIDWLEANRNPQ 119
                                    14        24     |  34        44 | |    54        64       | -    |   84        94  |   |104       114     
                                                    30-MSE          46-MSE           63-MSE   72     79                97-MSE                  
                                                                      48-MSE                                              101-MSE
   Legend:   → Mismatch (orange background)
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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 2IJL)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IJL)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A9CHN1_AGRFC | A9CHN1)
molecular function
    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.

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