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 STRUCTURE OF SALICYLATE 1,2-DIOXYGENASE FROM PSEUDOAMINOBACTER SALICYLATOXIDANS ADDUCTS WITH SALICYLATE
 
Authors :  M. Ferraroni, F. Briganti, I. Matera
Date :  18 Jun 10  (Deposition) - 13 Jul 11  (Release) - 21 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Beta-Sandwich, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Ferraroni, I. Matera, L. Steimer, S. Burger, A. Scozzafava, A. Stolz, F. Briganti
Crystal Structures Of Salicylate 1, 2-Dioxygenase-Substrates Adducts: A Step Towards The Comprehension Of The Structural Basis For Substrate Selection In Class Iii Ring Cleaving Dioxygenases.
J. Struct. Biol. V. 177 431 2012
PubMed-ID: 22155290  |  Reference-DOI: 10.1016/J.JSB.2011.11.026

(-) Compounds

Molecule 1 - GENTISATE 1,2-DIOXYGENASE
    Chains: A
    EC Number: 1.13.11.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PSEUDAMINOBACTER SALICYLATOXIDANS
    Organism Taxid: 93369
    Strain: BN12

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1FE21Ligand/IonFE (II) ION
2GOL2Ligand/IonGLYCEROL
3SAL1Ligand/Ion2-HYDROXYBENZOIC ACID
Biological Unit 1 (3, 16)
No.NameCountTypeFull Name
1FE24Ligand/IonFE (II) ION
2GOL8Ligand/IonGLYCEROL
3SAL4Ligand/Ion2-HYDROXYBENZOIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:119 , HIS A:121 , HIS A:160 , SAL A:370BINDING SITE FOR RESIDUE FE2 A 369
2AC2SOFTWARELEU A:38 , ARG A:83 , GLN A:108 , HIS A:119 , HIS A:121 , ARG A:127 , HIS A:160 , HIS A:162 , ASP A:174 , LEU A:176 , FE2 A:369BINDING SITE FOR RESIDUE SAL A 370
3AC3SOFTWARELEU A:219 , ARG A:265 , GLU A:282 , ARG A:295 , GLU A:297 , ARG A:347 , HOH A:412 , HOH A:417 , HOH A:498 , HOH A:526BINDING SITE FOR RESIDUE GOL A 371
4AC4SOFTWAREPRO A:56 , HIS A:57 , VAL A:58 , MET A:314 , GLU A:317 , HOH A:439BINDING SITE FOR RESIDUE GOL A 372

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NJZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NJZ)

(-) 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:364
 aligned with Q67FT0_PSESE | Q67FT0 from UniProtKB/TrEMBL  Length:368

    Alignment length:364
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363    
         Q67FT0_PSESE     4 EKLDHESVTQAMQPKDTPELRALYKSFEEESIIPLWTQLGDLMPIHPKSKAVPHVWKWSTLLRLARKSGELVPVGRGGERRALGLANPGLGGNAYISPTMWAGIQYLGPRETAPEHRHSQNAFRFVVEGEGVWTVVNGDPVRMSRGDLLLTPGWCFHGHHNDTDQPMAWIDGLDIPFSQQMDVGFFEFGSDRVTDYATPNFSRGERLWCHPGLRPLSGLQNTVASPIGAYRWEFTDRALTEQLLLEDEGQPATVAPGHAAIRYVNPTTGGDVMPTLRCEFHRLRAGTETATRNEVGSTVFQVFEGAGAVVMNGETTKLEKGDMFVVPSWVPWSLQAETQFDLFRFSDAPIMEALSFMRTKIEGQ 367
               SCOP domains d3njza_ A: automated matches                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhhh......hhhhhh..........eeehhhhhhhhhhhhhhhh.........eee................eeeeeee....eeeeeee...eeee......eeeee..eeee.....eeee.....eeeee.....eeeeeeehhhhhhhhh...eee.............hhhhhhhh.....hhhhh.........eehhhhhhhhhhhhhhhhhh.........eeeee..............eeeeeee........eee...eeeeeee..eeeee..eeeee....eeee.....eeeee...eeeeeeehhhhhhhh....eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3njz A   4 EKLDHESVTQAMQPKDTPELRALYKSFEEESIIPLWTQLGDLMPIHPKSKAVPHVWKWSTLLRLARKSGELVPVGRGGERRALGLANPGLGGNAYISPTMWAGIQYLGPRETAPEHRHSQNAFRFVVEGEGVWTVVNGDPVRMSRGDLLLTPGWCFHGHMNDTDQPMAWIDGLDIPFSQQMDVGFFEFGSDRVTDYATPNFSRGERLWCHPGLRPLSGLQNTVASPIGAYRWEFTDRALTEQLLLEDEGQPATVAPGHAAIRYVNPTTGGDVMPTLRCEFHRLRAGTETATRNEVGSTVFQVFEGAGAVVMNGETTKLEKGDMFVVPSWVPWSLQAETQFDLFRFSDAPIMEALSFMRTKIEGQ 367
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363
   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  (1, 1)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q67FT0_PSESE | Q67FT0)
molecular function
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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
    FE2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SAL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3njz)
 
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
  3njz
    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
  Q67FT0_PSESE | Q67FT0
    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)
  1.13.11.4
    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
  Q67FT0_PSESE | Q67FT0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q67FT0_PSESE | Q67FT0: 2phd 3nkt 3nl1 3nst 3nvc 3nw4 4fag 4fah 4fbf

(-) Related Entries Specified in the PDB File

2phd CRYSTAL STRUCTURE OF NATIVE SALICYLATE 1,2-DIOXYGENASE FROM PSEUDOAMINOBACTER SALICYLATOXIDANS
3nkt CRYSTAL STRUCTURE OF SALICYLATE 1,2-DIOXYGENASE FROM PSEUDOAMINOBACTER SALICYLATOXIDANS ADDUCTS WITH NAPHTHOATE
3nl1 CRYSTAL STRUCTURE OF SALICYLATE 1,2-DIOXYGENASE FROM PSEUDOAMINOBACTER SALICYLATOXIDANS ADDUCTS WITH GENTISATE
3nst CRYSTAL STRUCTURE OF SALICYLATE 1,2-DIOXYGENASE G106A MUTANT FROM PSEUDOAMINOBACTER SALICYLATOXIDANS