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
(-)Biological Unit 2
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF NON-HEME IRON OXYGENASE ORFP IN COMPLEX WITH FE, SUCCINATE, AND (3S)-HYDROXY-L-ARG
 
Authors :  C. Y. Chang, Y. C. Liu, S. Y. Lyu, C. C. Wu, T. L. Li
Date :  05 Aug 13  (Deposition) - 25 Jun 14  (Release) - 25 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.02
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Hydroxylase, Fe Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Y. Chang, S. Y. Lyu, Y. C. Liu, N. S. Hsu, C. C. Wu, C. F. Tang, K. H. Lin, J. Y. Ho, C. J. Wu, M. D. Tsai, T. L. Li
Biosynthesis Of Streptolidine Involved Two Unexpected Intermediates Produced By A Dihydroxylase And A Cyclase Through Unusual Mechanisms.
Angew. Chem. Int. Ed. Engl. V. 53 1943 2014
PubMed-ID: 24505011  |  Reference-DOI: 10.1002/ANIE.201307989

(-) Compounds

Molecule 1 - L-ARGININE BETA-HYDROXYLASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: STREPTOMYCES LAVENDULAE
    Organism Taxid: 58340
    Synonym: ORFP

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1AKG2Ligand/Ion2-OXOGLUTARIC ACID
2FE5Ligand/IonFE (III) ION
3SIN2Ligand/IonSUCCINIC ACID
4ZZU2Ligand/Ion(2S,3S)-3-HYDROXYARGININE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1AKG2Ligand/Ion2-OXOGLUTARIC ACID
2FE-1Ligand/IonFE (III) ION
3SIN-1Ligand/IonSUCCINIC ACID
4ZZU-1Ligand/Ion(2S,3S)-3-HYDROXYARGININE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1AKG-1Ligand/Ion2-OXOGLUTARIC ACID
2FE-1Ligand/IonFE (III) ION
3SIN2Ligand/IonSUCCINIC ACID
4ZZU2Ligand/Ion(2S,3S)-3-HYDROXYARGININE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:154 , GLU A:156 , HIS A:303 , AKG A:403 , HOH A:637BINDING SITE FOR RESIDUE FE A 401
02AC2SOFTWAREASP A:157 , HIS A:211 , HOH A:642 , HOH A:643 , HOH A:644BINDING SITE FOR RESIDUE FE A 402
03AC3SOFTWAREILE A:132 , LEU A:151 , HIS A:154 , GLU A:156 , THR A:180 , HIS A:303 , ARG A:305 , ARG A:317 , ARG A:321 , FE A:401 , HOH A:637 , HOH A:638BINDING SITE FOR RESIDUE AKG A 403
04AC4SOFTWAREHIS B:154 , GLU B:156 , HIS B:303 , AKG B:402 , HOH B:578BINDING SITE FOR RESIDUE FE B 401
05AC5SOFTWAREILE B:132 , GLU B:156 , LEU B:167 , THR B:180 , HIS B:303 , ARG B:305 , ARG B:317 , ARG B:321 , FE B:401 , HOH B:578BINDING SITE FOR RESIDUE AKG B 402
06AC6SOFTWAREHIS C:154 , GLU C:156 , HIS C:303 , SIN C:402 , ZZU C:403BINDING SITE FOR RESIDUE FE C 401
07AC7SOFTWAREILE C:132 , LEU C:151 , HIS C:154 , THR C:180 , HIS C:303 , ARG C:305 , ARG C:317 , ARG C:321 , FE C:401 , ZZU C:403 , HOH C:618BINDING SITE FOR RESIDUE SIN C 402
08AC8SOFTWAREGLN C:123 , LEU C:143 , GLY C:144 , HIS C:154 , GLU C:156 , ASP C:208 , SER C:210 , ASP C:255 , PHE C:258 , ARG C:321 , FE C:401 , SIN C:402BINDING SITE FOR RESIDUE ZZU C 403
09AC9SOFTWAREHIS D:154 , GLU D:156 , HIS D:303 , SIN D:402 , ZZU D:403BINDING SITE FOR RESIDUE FE D 401
10BC1SOFTWARELEU D:151 , HIS D:154 , THR D:180 , HIS D:303 , ARG D:305 , ARG D:317 , ARG D:321 , FE D:401 , ZZU D:403BINDING SITE FOR RESIDUE SIN D 402
11BC2SOFTWAREGLN D:123 , GLN D:142 , LEU D:143 , GLY D:144 , HIS D:154 , GLU D:156 , ASP D:208 , ASP D:255 , ARG D:321 , FE D:401 , SIN D:402 , HOH D:572BINDING SITE FOR RESIDUE ZZU D 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4M26)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Arg A:96 -Pro A:97
2Arg B:96 -Pro B:97
3Arg C:96 -Pro C:97
4Arg D:96 -Pro D:97

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M26)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M26)

(-) Exons   (0, 0)

(no "Exon" information available for 4M26)

(-) 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:336
                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhh...eeeee....hhhhhh..............hhhhhhhhhhhhhhhheeeee..hhhhh.eeee..hhhhh...........eeee...........eeeeeeee.....eeeeee.hhhhhhhhhhhhhh....ee..hhhhhhhhh....hhhhhhhhhhhhhhhhh.....eeee..eeee..hhh.ee....hhhhhhhhhhhhhhhhhh.eeee.....eeeee...eeeee............eeeeeeee.hhhhhhhhh......ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4m26 A   9 TPSYSLTPAEASAVAELTLELAAAYGSFGDPVLLRDLPRLAARLPEGVQDFLREFKLADRHGHTVIRGHDFDQRRIGPTPDHWRGRVRPGPEFPEELLLMLYSALLGEPFGWATQQDGHLVHDIFPIRSHENDQLGMGSKQLLTWHTEDAFHPYRSDYLILGALRNPDHVPTTVGELDLSSLSAEDIDVLFEPRYHIAPDESHLPKNNTIATEEEAARFATIQRMIDERPLGPLLYGSRLDPYMRLDPYFTSVPQDDTDARRAYDALFKVVDSGMREVVADQGDVLFIDNHRAVHGRLPFQARYDGTDRWLKRVCVTSDLRRSREMRATSATRLLG 344
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338      


Chain B from PDB  Type:PROTEIN  Length:314
                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhh...eeeee....hhhhhh..............hhhhhhhhhhhhhhhheeeee.hhhhhh..eee.................................eeeeeeee.....eeeee..hhhhhhhhhhhhhhh...ee...............eeee..eeee..hhh.ee....hhhhhhhhhhhhhhhhhhheeee.....eeeee....eeee............eeeeeeee.hhhhhhhhh......ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m26 B   9 TPSYSLTPAEASAVAELTLELAAAYGSFGDPVLLRDLPRLAARLPEGVQDFLREFKLADRHGHTVIRGHDFDQRRIGPTPDHWRGRVRPGPEFPEELLLMLYSALLGEPFGWATQQDGHLVHDIFPIRSHENDQLGMGSKQLLTWHTEDAFHPYRSDYLILGALRNPDHVPTTVGELDLSSLSAEDIDVLFEPRYHIAPDESMIDERPLGPLLYGSRLDPYMRLDPYFTSVPQDDTDARRAYDALFKVVDSGMREVVADQGDVLFIDNHRAVHGRLPFQARYDGTDRWLKRVCVTSDLRRSREMRATSATRLLG 344
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208 ||    240       250       260       270       280       290       300       310       320       330       340    
                                                                                                                                                                                                                                   210|                                                                                                               
                                                                                                                                                                                                                                    233                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:332
                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhh...eeeee....hhhhhh..............hhhhhhhhhhhhhhhheeeee.hhhhhh.eeee..hhhhh...........eeee...........eeeeeeee.....eeeee.......hhhhhhhhh....ee..hhhhh..........hhhhhhhhhhh.....eeee..eeee..hhh.ee....hhhhhhhhhhhhhhhhhh.eeee.....eeeee....eeee............eeeeeeee.hhhhhhhhh......ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m26 C   9 TPSYSLTPAEASAVAELTLELAAAYGSFGDPVLLRDLPRLAARLPEGVQDFLREFKLADRHGHTVIRGHDFDQRRIGPTPDHWRGRVRPGPEFPEELLLMLYSALLGEPFGWATQQDGHLVHDIFPIRSHENDQLGMGSKQLLTWHTEDAFHPYRSDYLILGALRNPDHVPTTVGELDLSSLSAEDIDVLFEPRYHIAPDESHLPKNNTIEAARFATIQRMIDERPLGPLLYGSRLDPYMRLDPYFTSVPQDDTDARRAYDALFKVVDSGMREVVADQGDVLFIDNHRAVHGRLPFQARYDGTDRWLKRVCVTSDLRRSREMRATSATRLLG 344
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218|      232       242       252       262       272       282       292       302       312       322       332       342  
                                                                                                                                                                                                                                           218|                                                                                                                         
                                                                                                                                                                                                                                            223                                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:336
                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhh...eeeee....hhhhhh..............hhhhhhhhhhhhhhhheeeee..hhhhh.eeee..hhhhh...........eeee...........eeeeeeee.....eeeee..hhhhhhhhhhhhhh....ee......hhhhh...........hhhhhhhhhh.....eeee..eeee..hhh.ee....hhhhhhhhhhhhhhhhhhheeee.....eeeee....eeee............eeeeeeee.hhhhhhhhh......ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4m26 D   9 TPSYSLTPAEASAVAELTLELAAAYGSFGDPVLLRDLPRLAARLPEGVQDFLREFKLADRHGHTVIRGHDFDQRRIGPTPDHWRGRVRPGPEFPEELLLMLYSALLGEPFGWATQQDGHLVHDIFPIRSHENDQLGMGSKQLLTWHTEDAFHPYRSDYLILGALRNPDHVPTTVGELDLSSLSAEDIDVLFEPRYHIAPDESHLPKNNTIATEEEAARFATIQRMIDERPLGPLLYGSRLDPYMRLDPYFTSVPQDDTDARRAYDALFKVVDSGMREVVADQGDVLFIDNHRAVHGRLPFQARYDGTDRWLKRVCVTSDLRRSREMRATSATRLLG 344
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338
   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 4M26)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M26)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M26)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

 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
    AKG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SIN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZZU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:96 - Pro A:97   [ RasMol ]  
    Arg B:96 - Pro B:97   [ RasMol ]  
    Arg C:96 - Pro C:97   [ RasMol ]  
    Arg D:96 - Pro D:97   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Biol. Unit 2 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
  4m26
    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
  G9MBV2_STRLA | G9MBV2
    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)
  (no 'Enzyme Classificator' available)
    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
  G9MBV2_STRLA | G9MBV2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        G9MBV2_STRLA | G9MBV2: 4m23 4m25 4m27 4m2c 4m2e 4m2f 4m2g 4m2i 4ne0

(-) Related Entries Specified in the PDB File

4m23 4m25 4m27 4m2c 4m2e 4m2f 4m2g 4m2i 4m2j 4m2k 4m2m