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(-) Description

Title :  RIBONUCLEOTIDE REDUCTASE Y122 2,3-F2Y VARIANT
 
Authors :  M. A. Funk, C. L. Drennan
Date :  10 Jul 15  (Deposition) - 22 Jun 16  (Release) - 13 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Unnatural Amino Acid, Fluorotyrosine, Ferritin Superfamily, Metalloenzyme, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. H. Oyala, K. R. Ravichandran, M. A. Funk, P. A. Stucky, T. A. Stich, C. L. Drennan, R. D. Britt, J. Stubbe
Biophysical Characterization Of Fluorotyrosine Probes Site-Specifically Incorporated Into Enzymes: E. Coli Ribonucleotide Reductase As An Example.
J. Am. Chem. Soc. V. 138 7951 2016
PubMed-ID: 27276098  |  Reference-DOI: 10.1021/JACS.6B03605

(-) Compounds

Molecule 1 - RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1, BETA SUBUNIT, FERRITIN-LIKE PROTEIN
    Chains: A
    EC Number: 1.17.4.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: NRDB, EC1303_C24130
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI 1303
    Organism Taxid: 745156

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2FEO1Ligand/IonMU-OXO-DIIRON
3FY21Mod. Amino Acid2,3-DIFLUORO-L-TYROSINE
4SO44Ligand/IonSULFATE ION
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FEO2Ligand/IonMU-OXO-DIIRON
3FY22Mod. Amino Acid2,3-DIFLUORO-L-TYROSINE
4SO48Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:84 , GLU A:115 , HIS A:118 , GLU A:204 , GLU A:238 , HIS A:241 , HOH A:547 , HOH A:591binding site for residue FEO A 401
2AC2SOFTWAREPRO A:66 , GLU A:67 , SER A:295 , HOH A:503 , HOH A:553 , HOH A:646binding site for residue SO4 A 402
3AC3SOFTWAREARG A:221 , LEU A:223 , HOH A:661binding site for residue SO4 A 403
4AC4SOFTWAREGLN A:145 , LYS A:148 , ARG A:149 , ASP A:285 , HOH A:537binding site for residue SO4 A 404
5AC5SOFTWAREARG A:236 , SER A:341 , ASP A:342 , ASN A:343binding site for residue SO4 A 405
6AC6SOFTWAREARG A:253binding site for residue CL A 407
7AC7SOFTWAREARG A:27 , TYR A:28 , ASP A:29 , LEU A:77 , GLN A:80 , THR A:81 , ASP A:84 , HIS A:118 , SER A:119 , ARG A:120 , SER A:121 , HIS A:124 , ILE A:125 , ILE A:126 , ARG A:127 , PHE A:137 , PHE A:208 , ILE A:231 , ILE A:234 , HOH A:525binding site for Ligand residues FY2 A 122 through THR A 123 bound to SER A 121
8AC8SOFTWARELEU A:77 , GLN A:80 , THR A:81 , ASP A:84 , HIS A:118 , SER A:119 , ARG A:120 , SER A:121 , THR A:123 , HIS A:124 , ILE A:125 , ILE A:126 , PHE A:208 , ILE A:231 , ILE A:234binding site for Ligand FY2 A 122 bound to SER A 121

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CI1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5CI1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CI1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CI1)

(-) Exons   (0, 0)

(no "Exon" information available for 5CI1)

(-) 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    
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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:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................................hhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee..eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh............hhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ci1 A   1 AYTTFSQTKNDQLKEPMFFGQPVNVARYDQQKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSxTHIIRNIVNDPSVVFDDIVTNEQIQKRAEGISSYYDELIEMTSYWHLLGEGTHTVNGKTVTVSLRELKKKLYLCLMSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLLRSGADDPEMAEIAEECKQECYDLFVQAAQQEKDWADYLFRDGSMIGLNKDILCQYVEYITNIRMQAVGLDLPFQTRSNPIPWINTWLVSDNVQVAPQ 349
                                    10        20        30        40        50        60        70        80        90       100       110       120 |     130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340         
                                                                                                                                                   122-FY2
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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 5CI1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CI1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CI1)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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        A0A0E1LZC3_E | A0A0E1LZC3: 5ci0 5ci4

(-) Related Entries Specified in the PDB File

5ci0 5ci2 5ci3 5ci4