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(-) Description

Title :  CRYSTAL STRUCTURE OF MAGNETOSPIRILLUM GRYPHISWALDENSE MSR-1 FUR-MN2+-FEOAB1 OPERATOR
 
Authors :  Z. Deng, Z. Chen
Date :  12 Sep 14  (Deposition) - 15 Jul 15  (Release) - 15 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ferric Uptake Regulator (Fur), Metal Ion Activation, Operator Recognition, Cooperativity, Broad Substrate Recognition, Dna Shape Readout, Metal Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Deng, Q. Wang, Z. Liu, M. Zhang, A. C. Machado, T. P. Chiu, C. Feng, Q. Zhang, L. Yu, L. Qi, J. Zheng, X. Wang, X. Huo, X. Qi, X. Li, W. Wu, R. Rohs, Y. Li, Z. Chen
Mechanistic Insights Into Metal Ion Activation And Operator Recognition By The Ferric Uptake Regulator.
Nat Commun V. 6 7642
PubMed-ID: 26134419  |  Reference-DOI: 10.1038/NCOMMS8642

(-) Compounds

Molecule 1 - DNA (25-MER)
    Chains: A
    Engineered: YES
    Synonym: FEOAB1 OPERATOR
    Synthetic: YES
 
Molecule 2 - DNA (25-MER)
    Chains: B
    Engineered: YES
    Synonym: FEOAB1 OPERATOR
    Synthetic: YES
 
Molecule 3 - DNA-BINDING TRANSCRIPTIONAL DUAL REGULATOR OF SIDEROPHORE BIOSYNTHESIS AND TRANSPORT(FUR FAMILY)
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: FUR, MGMSRV2_3137
    Mutation: YES
    Organism Scientific: MAGNETOSPIRILLUM GRYPHISWALDENSE
    Organism Taxid: 1430440
    Strain: MSR-1 V2

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1MN4Ligand/IonMANGANESE (II) ION
2SO41Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS C:87 , ASP C:89 , GLU C:108 , HIS C:125 , HOH C:306BINDING SITE FOR RESIDUE MN C 200
2AC2SOFTWAREHIS C:33 , GLU C:81 , HIS C:88 , HIS C:90 , GLU C:101BINDING SITE FOR RESIDUE MN C 201
3AC3SOFTWAREHIS D:87 , ASP D:89 , GLU D:108 , HIS D:125 , HOH D:304BINDING SITE FOR RESIDUE MN D 201
4AC4SOFTWAREHIS D:33 , GLU D:81 , HIS D:88 , HIS D:90 , GLU D:101BINDING SITE FOR RESIDUE MN D 202
5AC5SOFTWAREASP D:32 , HIS D:33 , ARG D:79 , ARG D:98 , VAL D:99BINDING SITE FOR RESIDUE SO4 D 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RB3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4RB3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RB3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RB3)

(-) Exons   (0, 0)

(no "Exon" information available for 4RB3)

(-) 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:DNA  Length:25
                                                         
                 4rb3 A   1 TTAATTGCAAATCATTTGCAATTGC  25
                                    10        20     


Chain B from PDB  Type:DNA  Length:25
                                                         
                 4rb3 B   1 GCAATTGCAAATGATTTGCAATTAA  25
                                    10        20     


Chain C from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhhhh.....hhhhhhhhhhhhhhh..eeee.......eeee......eeeee.....eeee.hhhhhhhhhhhhhhh.eeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rb3 C   1 MVSRIEQRLIDKGLKVTDQRRVIAQVLSDSADHPDVEEVYRRATAKDPRISIATVYRTVRLFEEESILERHDFGDGRARYEEAPSEHHDHLIDVNSARVIEFTSPEIEALQREIARKHGFRLVGHRLELYGVPLTS 136
                                    10        20        30        40        50        60        70        80        90       100       110       120       130      


Chain D from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhhhhhh..eeee.......eeee......eeeee.....eeee.hhhhhhhhhhhhhhh.eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rb3 D   2 VSRIEQRLIDKGLKVTDQRRVIAQVLSDSADHPDVEEVYRRATAKDPRISIATVYRTVRLFEEESILERHDFGDGRARYEEAPSEHHDHLIDVNSARVIEFTSPEIEALQREIARKHGFRLVGHRLELYGVPL 134
                                    11        21        31        41        51        61        71        81        91       101       111       121       131
   Legend:   → Mismatch (orange background)
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    → 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 4RB3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RB3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RB3)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        V6F4Q0_9PROT | V6F4Q0: 4ray 4raz 4rb0 4rb1 4rb2

(-) Related Entries Specified in the PDB File

4ray 4raz 4rb0 4rb1 4rb2