Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURES AND SITE-DIRECTED MUTAGENESIS STUDY OF NITROALKANE OXIDASE FROM STREPTOMYCES ANSOCHROMOGENES
 
Authors :  Y. H. Li, Z. Q. Gao, H. F. Hou
Date :  08 Jan 08  (Deposition) - 13 Jan 09  (Release) - 10 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Tim Barrel, Oxidoreductase, Dioxygenase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. H. Li, Z. Q. Gao, H. F. Hou, L. Li, J. H. Zhang, H. H. Yang, Y. H. Dong, H. R. Tan
Crystal Structure And Site-Directed Mutagenesis Of A Nitroalkane Oxidase From Streptomyces Ansochromogenes
Biochem. Biophys. Res. Commun. V. 405 344 2011
PubMed-ID: 21147069  |  Reference-DOI: 10.1016/J.BBRC.2010.12.050

(-) Compounds

Molecule 1 - 2-NITROPROPANE DIOXYGENASE
    Chains: A
    EC Number: 1.7.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET23B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: 2-NPDL
    Organism Scientific: STREPTOMYCES ANSOCHROMOGENES
    Organism Taxid: 115647
    Strain: 7100

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
2MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
2MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:16 , PRO A:17 , MET A:18 , ALA A:19 , ASN A:68 , PHE A:70 , HIS A:129 , GLN A:172 , ALA A:176 , GLY A:177 , GLY A:215 , GLY A:216 , GLN A:235 , GLY A:237 , THR A:238 , TRP A:320 , GLY A:322 , HOH A:372 , HOH A:377 , HOH A:378 , HOH A:387 , HOH A:389 , HOH A:417BINDING SITE FOR RESIDUE FMN A 370
2AC2SOFTWARETRP A:95 , ASP A:112 , ASP A:134 , ARG A:281 , GLU A:285 , HOH A:514BINDING SITE FOR RESIDUE MPD A 371

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BW2)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr A:294 -Pro A:295

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BW2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BW2)

(-) Exons   (0, 0)

(no "Exon" information available for 3BW2)

(-) 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:347
 aligned with Q9FDD4_9ACTN | Q9FDD4 from UniProtKB/TrEMBL  Length:363

    Alignment length:350
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352
         Q9FDD4_9ACTN     3 SALTDLFPLPIVQAPMAGGVSVPQLAAAVCEAGGLGFLAAGYKTADGMYQEIKRLRGLTGRPFGVNVFMPQPELAESGAVEVYAHQLAGEAAWYETELGDPDGGRDDGYDAKLAVLLDDPVPVVSFHFGVPDREVIARLRRAGTLTLVTATTPEEARAVEAAGADAVIAQGVEAGGHQGTHRDSSEDDGAGIGLLSLLAQVREAVDIPVVAAGGIMRGGQIAAVLAAGADAAQLGTAFLATDESGAPGPHKRALTDPLFARTRLTRAFTGRPARSLVNRFLREHGPYAPAAYPDVHHLTSPLRKAAAKAGDAQGMALWAGQGHRMARELPAGRLVEVLAAELAEARTALS 352
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee........hhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhh...eeeeee......---hhhhhhhhhhhhhhhhh.............hhhhhhhhhhhh...eeeee....hhhhhhhhhhh..eeeeee.hhhhhhhhhhh...eeeee.....ee......hhhhh....hhhhhhhhhhhhh...eeee....hhhhhhhhhhh...eeeehhhhhh......hhhhhhhhhhhhhh.eeee.......eeee.hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh......hhhhh...hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bw2 A   3 SALTDLFPLPIVQAPMAGGVSVPQLAAAVCEAGGLGFLAAGYKTADGMYQEIKRLRGLTGRPFGVNVFMPQPEL---GAVEVYAHQLAGEAAWYETELGDPDGGRDDGYDAKLAVLLDDPVPVVSFHFGVPDREVIARLRRAGTLTLVTATTPEEARAVEAAGADAVIAQGVEAGGHQGTHRDSSEDDGAGIGLLSLLAQVREAVDIPVVAAGGIMRGGQIAAVLAAGADAAQLGTAFLATDESGAPGPHKRALTDPLFARTRLTRAFTGRPARSLVNRFLREHGPYAPAAYPDVHHLTSPLRKAAAKAGDAQGMALWAGQGHRMARELPAGRLVEVLAAELAEARTALS 352
                                    12        22        32        42        52        62        72   |   |82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352
                                                                                                    76  80
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 3BW2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3BW2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BW2)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9FDD4_9ACTN | Q9FDD4)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0018580    nitronate monooxygenase activity    Catalysis of the reaction: ethylnitronate + O(2) = acetaldehyde + nitrite.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    FMN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MPD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Tyr A:294 - Pro A:295   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3bw2
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q9FDD4_9ACTN | Q9FDD4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  1.7.3.1
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q9FDD4_9ACTN | Q9FDD4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9FDD4_9ACTN | Q9FDD4: 3bw3 3bw4

(-) Related Entries Specified in the PDB File

3bw3 3bw4