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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DEPH
 
Authors :  J. Li, C. Wang, Z. M. Zhang, J. H. Zhou, E. Cheng
Date :  14 Mar 13  (Deposition) - 09 Apr 14  (Release) - 15 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Disulfide Bond Formation, Fk228, Depsipeptide, Fad-Dependent Oxidoreductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Li, C. Wang, Z. M. Zhang, Y. Q. Cheng, J. Zhou
The Structural Basis Of An Nadp+-Independent Dithiol Oxidas In Fk228 Biosynthesis.
Sci Rep V. 4 4145 2014
PubMed-ID: 24553401  |  Reference-DOI: 10.1038/SREP04145

(-) Compounds

Molecule 1 - DEPH
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DEPH
    Organism Scientific: CHROMOBACTERIUM VIOLACEUM
    Organism Taxid: 536
    Strain: NO. 968

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 11)

Asymmetric/Biological Unit (5, 11)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
3FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
4MG1Ligand/IonMAGNESIUM ION
5PO41Ligand/IonPHOSPHATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:54 , GLY A:55 , SER A:57 , HIS A:58 , ALA A:59 , ILE A:77 , ASP A:78 , ALA A:79 , GLY A:80 , ALA A:81 , ARG A:83 , ASN A:84 , SER A:90 , HIS A:91 , ASP A:123 , SER A:124 , VAL A:125 , PHE A:154 , GLY A:155 , ASP A:158 , CYS A:180 , HIS A:181 , SER A:273 , GLY A:310 , ASP A:311 , GLY A:317 , THR A:318 , VAL A:319 , CL A:402 , EDO A:407 , HOH A:501 , HOH A:502 , HOH A:507 , HOH A:514 , HOH A:517 , HOH A:537 , HOH A:560 , HOH A:562 , HOH A:610BINDING SITE FOR RESIDUE FAD A 401
02AC2SOFTWAREHIS A:176 , CYS A:177 , FAD A:401BINDING SITE FOR RESIDUE CL A 402
03AC3SOFTWARESER A:90 , HIS A:91 , GLY A:92 , VAL A:93 , GLN A:96BINDING SITE FOR RESIDUE MG A 403
04AC4SOFTWAREVAL A:238 , ARG A:239 , ASP A:240 , ARG A:257BINDING SITE FOR RESIDUE PO4 A 404
05AC5SOFTWAREGLN A:66 , HOH A:690 , HIS B:91 , CYS B:180 , FAD B:401 , HOH B:508 , HOH B:659BINDING SITE FOR RESIDUE EDO A 405
06AC6SOFTWAREASP A:158 , GLU A:167 , HOH A:521BINDING SITE FOR RESIDUE EDO A 406
07AC7SOFTWAREEDO A:405 , ILE B:54 , GLY B:55 , SER B:57 , HIS B:58 , ALA B:59 , ILE B:77 , ASP B:78 , ALA B:79 , GLY B:80 , ALA B:81 , ARG B:83 , ASN B:84 , SER B:90 , HIS B:91 , ASP B:123 , SER B:124 , VAL B:125 , PHE B:154 , GLY B:155 , ASP B:158 , CYS B:180 , HIS B:181 , SER B:273 , GLY B:310 , ASP B:311 , GLY B:317 , THR B:318 , VAL B:319 , CL B:402 , HOH B:501 , HOH B:503 , HOH B:508 , HOH B:509 , HOH B:523 , HOH B:549 , HOH B:551 , HOH B:552 , HOH B:628BINDING SITE FOR RESIDUE FAD B 401
08AC8SOFTWAREHIS A:91 , GLY A:92 , CYS A:180 , THR A:318 , FAD A:401 , HOH A:514 , GLN B:66BINDING SITE FOR RESIDUE EDO A 407
09AC9SOFTWAREHIS B:176 , CYS B:177 , HIS B:181 , FAD B:401BINDING SITE FOR RESIDUE CL B 402
10BC1SOFTWAREALA B:87 , SER B:88 , GLN B:89 , GLY B:171 , GLU B:172 , HOH B:611 , HOH B:677BINDING SITE FOR RESIDUE EDO B 403
11BC2SOFTWAREILE A:94 , GLY A:95 , GLN A:96 , ILE B:94 , GLY B:95 , GLN B:96BINDING SITE FOR RESIDUE EDO B 404

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:177 -A:180
2B:177 -B:180

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JN9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JN9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JN9)

(-) Exons   (0, 0)

(no "Exon" information available for 4JN9)

(-) 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:299
                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee..hhhhhhhhhhhhhh...eeeee.....................hhhhhhhhhhhhhhh...eeeee..eeeeeee..eeeeee....eeeeeeeee...eeee......hhhhh...ee.hhhhhhhhhh..eeeee...hhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhh.eee...eeeee...eeee....eee..eeee..eeee..hhhhhh...eeee..eeee............eee.hhhh....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jn9 A  42 SETSPMLFDVIVIGGSHAGQSAALQIARARRRVLVIDAGARRNRFASQSHGVIGQDGRSPDAIAADGKAQLLAYPNAQWREDSVVRAERSDAGYTLICASGQHYRACQLVLAFGVVDELPELEGLEERWGESVFHCPYCHGYELDGGRIGVLGSGPLSYLSAMLMPEWGQTVFLTDASFEPDEEQREALARRGVEIVRDRIARIVDRATVELADGRRIAFDGLFTMNRMRLSSPVAEQLGCAIEEGPLGPYVRTDDAMETSTPGVFACGDITHRGGTVALAIGNGALAGIAAHRKLVFG 340
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331         


Chain B from PDB  Type:PROTEIN  Length:294
                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhh...eeeee.....................hhhhhhhhhhhhhhh...eeeee..eeeeeee..eeeeee....eeeeeeeee...eeee......hhhhh...ee.hhhhhhhhhheeeeeee..hhhhhhhhhhh...eeeeee.......hhhhhhhhhh...eee...eeeee..eeeee....eeee.eeee..eeee..hhhhhh...eeee..eeee............eee.hhhh....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jn9 B  47 MLFDVIVIGGSHAGQSAALQIARARRRVLVIDAGARRNRFASQSHGVIGQDGRSPDAIAADGKAQLLAYPNAQWREDSVVRAERSDAGYTLICASGQHYRACQLVLAFGVVDELPELEGLEERWGESVFHCPYCHGYELDGGRIGVLGSGPLSYLSAMLMPEWGQTVFLTDASFEPDEEQREALARRGVEIVRDRIARIVDRATVELADGRRIAFDGLFTMNRMRLSSPVAEQLGCAIEEGPLGPYVRTDDAMETSTPGVFACGDITHRGGTVALAIGNGALAGIAAHRKLVFG 340
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336
   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 4JN9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JN9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JN9)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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4jna