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(-) Description

Title :  STRUCTURE OF THE FAD AND HEME BINDING PROTEIN MSMEG_4975 FROM MYCOBACTERIUM SMEGMATIS
 
Authors :  F. H. Ahmed, P. D. Carr, C. J. Jackson
Date :  18 Feb 15  (Deposition) - 21 Oct 15  (Release) - 04 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Fad, Heme, Split Beta-Barrel (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. H. Ahmed, P. D. Carr, B. M. Lee, L. Afriat-Jurnou, A. E. Mohamed, N. S. Hong, J. Flanagan, M. C. Taylor, C. Greening, C. J. Jackson
Sequence-Structure-Function Classification Of A Catalytically Diverse Oxidoreductase Superfamily In Mycobacteria.
J. Mol. Biol. V. 427 3554 2015
PubMed-ID: 26434506  |  Reference-DOI: 10.1016/J.JMB.2015.09.021

(-) Compounds

Molecule 1 - FLAVIN-NUCLEOTIDE-BINDING PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: MSMEG_4975, MSMEI_4848, LJ00_24605
    Organism Scientific: MYCOBACTERIUM SMEGMATIS (STRAIN ATCC 700084 / MC(2)155)
    Organism Taxid: 246196
    Strain: ATCC 700084 / MC(2)155
    Synonym: PYRIDOXAMINE 5'-PHOSPHATE OXIDASE-RELATED,FMN-BINDING PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric/Biological Unit (5, 9)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4NI2Ligand/IonNICKEL (II) ION
5SO42Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:121 , ASP A:125 , SO4 A:302 , GLY B:57 , HOH B:449binding site for residue NI A 301
2AC2SOFTWAREARG A:121 , ASP A:125 , NI A:301 , HOH A:458 , ARG B:55 , GLY B:57binding site for residue SO4 A 302
3AC3SOFTWAREVAL A:56 , TYR A:123 , HOH A:406 , HOH A:426 , HOH A:496 , GLY B:122 , TYR B:123 , HOH B:469binding site for residue ACT A 303
4AC4SOFTWAREHIS A:63 , SER A:65 , LEU A:124 , THR A:128 , PHE A:131 , SER A:142 , ALA A:149 , THR A:150 , HOH A:490 , HOH A:510 , SER B:96 , PHE B:97 , SER B:99 , SER B:100 , PHE B:101 , TYR B:103 , LYS B:165 , FAD B:302 , HOH B:405binding site for residue HEM A 304
5AC5SOFTWAREARG A:14 , LEU A:15 , LYS A:18 , SER A:96 , PHE A:97 , SER A:99 , SER A:100 , PHE A:101 , TYR A:103 , LYS A:165 , HOH A:422 , HOH A:539 , HIS B:63 , SER B:65 , THR B:128 , PHE B:131 , SER B:142 , ALA B:149 , THR B:150 , FAD B:305 , HOH B:472 , HOH B:522binding site for residue HEM B 301
6AC6SOFTWARELEU A:35 , PRO A:50 , ILE A:51 , GLY A:52 , HIS A:63 , GLY A:64 , SER A:68 , PRO A:69 , TRP A:70 , HEM A:304 , HOH A:425 , GLN B:19 , TYR B:103 , SER B:105 , THR B:107 , PHE B:109 , SER B:163 , LYS B:165 , HOH B:405 , HOH B:511binding site for residue FAD B 302
7AC7SOFTWAREASP B:125 , SO4 B:304binding site for residue NI B 303
8AC8SOFTWAREARG A:55 , GLY A:57 , HOH A:447 , ARG B:121 , ASP B:125 , NI B:303binding site for residue SO4 B 304
9AC9SOFTWARESER A:9 , THR A:10 , ARG A:11 , VAL A:12 , THR A:13 , ARG A:14 , TYR A:103 , SER A:105 , THR A:107 , SER A:163 , LYS A:165 , LEU B:35 , PHE B:49 , PRO B:50 , ILE B:51 , GLY B:52 , HIS B:63 , GLY B:64 , SER B:68 , PRO B:69 , TRP B:70 , HEM B:301 , HOH B:425 , HOH B:436 , HOH B:453 , HOH B:491 , HOH B:495binding site for residue FAD B 305

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YBN)

(-) 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:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh..hhhhhhhhhh...eeeeeeee..eeeeeeee.eee..eeeeeee..hhhhhhhhh...eeeeeeeeeeeee.......eeeeeeeeeee..ee.hhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhheeeeeee.....eeeeee......hhhhhhh....eeeeeeeee...ee..........hhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ybn A   9 STRVTRLDEKQSTSRERLDDLLDTIPLATVALVRDGHPVAFPIGFGRVGDELVIHGSTGSPWLRALAEGAPAAVSVTALDGVVVARSSFESSFRYRSATLFGTFEVIADDAKRGYLDALTDRFIPGRTAELRASTRKELAATLALALAIGDDNWSLKLSEGWPDDADEDIAAGGWAGVVPLTTQYGAPLTAPDVAAGTPLPPSVRGMTGELRNT 222
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218    


Chain B from PDB  Type:PROTEIN  Length:205
                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhhhhhh...eeeeeeee..eeeeeeee.eee..eeeeeee..hhhhhhhhh..eeeeeeeeeeeeee.......eeeeeeeeeeee.ee.hhhhhhhhhhhhhhhhh..........hhhhhhheeeeeee.....eeeeee......hhhhhhhh...eeeeeeeee...ee..........hhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ybn B  17 EKQSTSRERLDDLLDTIPLATVALVRDGHPVAFPIGFGRVGDELVIHGSTGSPWLRALAEGAPAAVSVTALDGVVVARSSFESSFRYRSATLFGTFEVIADDAKRGYLDALTDRFIPGRTAELRASTRKELAATLALALAIGDDNWSLKLSEGWPDDADEDIAAGGWAGVVPLTTQYGAPLTAPDVAAGTPLPPSVRGMTGELRN 221
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216
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  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 4YBN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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