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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FLAVOHEM-LIKE-FAD/NAD BINDING DOMAIN OF NITRIC OXIDE DIOXYGENASE FROM VIBRIO CHOLERAE O1 BIOVAR EL TOR
 
Authors :  Y. Kim, M. Gu, J. Hasseman, W. F. Anderson, A. Joachimiak, Center For S Genomics Of Infectious Diseases (Csgid)
Date :  02 Apr 12  (Deposition) - 25 Apr 12  (Release) - 25 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  Structural Genomics, Niaid, National Institute Of Allergy And Infectious Diseases, Center For Structural Genomics Of Infectious Diseases, Csgid, Alpha-Beta-Alpha Sandwich, Beta Structure, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, M. Gu, J. Hasseman, W. F. Anderson, A. Joachimiak
Crystal Structure Of The Flavohem-Like-Fad/Nad Binding Domain Of Nitric Oxide Dioxygenase From Vibrio Cholerae O1 Biovar El Tor
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - FLAVOHEMOPROTEIN
    Chains: A, B
    EC Number: 1.14.12.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21 MAGIC
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: FAD_NAD(P)H BINDING DOMAIN, UNP RESIDUES 152-394
    Gene: HMP, VC_A0183
    Organism Scientific: VIBRIO CHOLERAE O1 BIOVAR EL TOR
    Organism Taxid: 243277
    Strain: N16961
    Synonym: FLAVOHEMOGLOBIN, HEMOGLOBIN-LIKE PROTEIN, NITRIC OXIDE DIOXYGENASE, NO OXYGENASE, NOD

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
1CL5Ligand/IonCHLORIDE ION
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3GOL5Ligand/IonGLYCEROL
4SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3GOL5Ligand/IonGLYCEROL
4SO42Ligand/IonSULFATE ION
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3GOL2Ligand/IonGLYCEROL
4SO42Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:40 , ARG A:56 , GLN A:57 , TYR A:58 , SER A:59 , SER A:72 , VAL A:73 , LYS A:74 , GLU A:76 , ASN A:82 , GLY A:84 , LEU A:85 , VAL A:86 , SER A:87 , THR A:128 , GLU A:234 , PHE A:236 , HOH A:422 , HOH A:436 , HOH A:457 , HOH A:467 , ASP B:3 , ARG B:5 , ARG B:53 , TYR B:103 , HOH B:538BINDING SITE FOR RESIDUE FAD A 301
02AC2SOFTWAREASP A:98 , SER A:99BINDING SITE FOR RESIDUE CL A 302
03AC3SOFTWAREARG A:2 , GLY A:4 , LEU A:102 , TYR A:103 , ALA A:104BINDING SITE FOR RESIDUE SO4 A 303
04AC4SOFTWAREASP A:108 , PHE A:109 , TYR A:233BINDING SITE FOR RESIDUE SO4 A 304
05AC5SOFTWAREARG A:114 , HOH A:491BINDING SITE FOR RESIDUE CL A 305
06AC6SOFTWARELYS A:142 , SER A:143BINDING SITE FOR RESIDUE GOL A 306
07AC7SOFTWAREASN A:152BINDING SITE FOR RESIDUE CL A 307
08AC8SOFTWARETYR A:89 , ASN A:93 , HOH A:462 , HOH A:504BINDING SITE FOR RESIDUE GOL A 308
09AC9SOFTWAREGLU B:48 , TYR B:89 , ASN B:93 , HOH B:516 , HOH B:535 , HOH B:596BINDING SITE FOR RESIDUE GOL B 401
10BC1SOFTWARETYR B:40 , ARG B:56 , GLN B:57 , TYR B:58 , SER B:59 , SER B:72 , VAL B:73 , LYS B:74 , GLU B:76 , GLY B:84 , LEU B:85 , VAL B:86 , SER B:87 , VAL B:125 , THR B:128 , PHE B:236 , HIS B:239 , HOH B:511 , HOH B:523 , HOH B:564 , HOH B:565 , HOH B:572BINDING SITE FOR RESIDUE FAD B 402
11BC2SOFTWAREALA A:168 , ASP B:108 , PHE B:109 , PHE B:110 , VAL B:112 , ARG B:114 , TYR B:206 , HIS B:232BINDING SITE FOR RESIDUE GOL B 403
12BC3SOFTWAREPRO A:238 , TYR B:40 , ILE B:41 , GLY B:42 , GLN B:57 , ALA B:104 , ALA B:106BINDING SITE FOR RESIDUE GOL B 404
13BC4SOFTWARELYS B:74 , VAL B:125BINDING SITE FOR RESIDUE CL B 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EH1)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:237 -Pro A:238

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EH1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EH1)

(-) Exons   (0, 0)

(no "Exon" information available for 4EH1)

(-) 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    
   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:237
                                                                                                                                                                                                                                                                             
               SCOP domains d4eh1a1 A:2-110 automated matches                                                                            d4eh1a2 A:111-238 automated matches                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee....eeeeeeee.............eeeeee........eeeeee.........eeeeee.........hhhhhhhhhhh....eeeeeeee...........eeeeee..hhhhhhhhhhhhhhh....eeeeeee.hhhhh.hhhhhhhhhhhhh.eeeeee........ee...............eeeeeehhhhhhhhhhhhhhhh.hhh.eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eh1 A   2 RDGRTFVVREKQVESAYVTSFVLVPADGGAVLDYQPGQYIGIEVTPEGSDYREIRQYSLSHASNGREYRISVKREGVGSDNPGLVSHYLHNNVKVGDSVKLYAPAGDFFYVERERPVVLISAGVGATPMQAILHTLAKQNKSGVTYLYACNSAKEHTFAQETAQLIAQQGWMQQVWYRDESADDVLQGEMQLAELILPIEDGDFYLCGPIGFMQYVVKQLLALGVDKARIHYEVFGP 238
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       


Chain B from PDB  Type:PROTEIN  Length:237
                                                                                                                                                                                                                                                                             
               SCOP domains d4eh1b1 B:3-110 automated matches                                                                           d4eh1b2 B:111-239 automated matches                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee....eeeeeeee.............eeeeee........eeeeee.........eeeeee.........hhhhhhhhhhh....eeeeeeee...........eeeeee..hhhhhhhhhhhhhhhh...eeeeeee.hhhhh.hhhhhhhhhhhhh.eeeeee.......eee...............eeeee.hhhhhhhhhhhhhhhh.hhh.eeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eh1 B   3 DGRTFVVREKQVESAYVTSFVLVPADGGAVLDYQPGQYIGIEVTPEGSDYREIRQYSLSHASNGREYRISVKREGVGSDNPGLVSHYLHNNVKVGDSVKLYAPAGDFFYVERERPVVLISAGVGATPMQAILHTLAKQNKSGVTYLYACNSAKEHTFAQETAQLIAQQGWMQQVWYRDESADDVLQGEMQLAELILPIEDGDFYLCGPIGFMQYVVKQLLALGVDKARIHYEVFGPH 239
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232
   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  (2, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EH1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EH1)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)

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