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

(-) Description

Title :  CRYSTAL STRUCTURE OF PHZG FROM PSEUDOMONAS FLUORESCENS 2-79 IN COMPLEX WITH A SECOND FMN IN THE SUBSTRATE BINDING SITE
 
Authors :  N. N. Xu, E. G. Ahuja, W. Blankenfeldt
Date :  18 Oct 12  (Deposition) - 07 Aug 13  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.33
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Excess Fmn, Substrate Mimic, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Xu, E. G. Ahuja, P. Janning, D. V. Mavrodi, L. S. Thomashow, W. Blankenfeldt
Trapped Intermediates In Crystals Of The Fmn-Dependent Oxidase Phzg Provide Insight Into The Final Steps Of Phenazine Biosynthesis
Acta Crystallogr. , Sect. D V. 69 1403 2013
PubMed-ID: 23897464  |  Reference-DOI: 10.1107/S0907444913008354

(-) Compounds

Molecule 1 - PHENAZINE BIOSYNTHESIS PROTEIN PHZG
    Chains: A, B
    EC Number: 1.4.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: ROSETTA 2 PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PHZG
    Organism Scientific: PSEUDOMONAS FLUORESCENS
    Organism Taxid: 294
    Strain: 2-79

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1FMN3Ligand/IonFLAVIN MONONUCLEOTIDE
2SO44Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:73 , ILE A:74 , VAL A:75 , VAL A:76 , SER A:88 , THR A:89 , SER A:93 , GLN A:94 , LYS A:95 , GLN A:152 , SER A:153 , HOH A:407 , HOH A:412 , HOH A:424 , HOH A:456 , HOH A:460 , LEU B:19 , TYR B:110 , GLN B:117 , TRP B:195 , ARG B:205 , HOH B:423BINDING SITE FOR RESIDUE FMN A 301
2AC2SOFTWAREGLN A:67 , ARG A:69 , ARG A:188 , HOH B:696BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWAREGLN A:31 , LEU A:33 , ARG A:219 , HOH A:592 , HOH A:678BINDING SITE FOR RESIDUE SO4 A 303
4AC4SOFTWAREARG A:57 , SER A:78 , GLU A:79 , ILE A:80 , HOH A:555BINDING SITE FOR RESIDUE SO4 A 304
5AC5SOFTWARETYR A:110 , GLN A:117 , TRP A:195 , ARG A:205 , HOH A:414 , ARG B:73 , ILE B:74 , VAL B:75 , VAL B:76 , SER B:88 , THR B:89 , SER B:93 , GLN B:94 , LYS B:95 , GLN B:152 , SER B:153 , FMN B:302 , HOH B:417 , HOH B:434 , HOH B:436 , HOH B:458 , HOH B:492BINDING SITE FOR RESIDUE FMN B 301
6AC6SOFTWARETRP A:195 , HIS A:203 , ARG B:57 , VAL B:76 , SER B:88 , ARG B:139 , TYR B:182 , FMN B:301 , HOH B:631 , HOH B:685BINDING SITE FOR RESIDUE FMN B 302
7AC7SOFTWAREARG B:57 , SER B:78 , GLU B:79 , ILE B:80BINDING SITE FOR RESIDUE SO4 B 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:174 -Pro A:175

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HMS)

(-) 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:202
                                                                                                                                                                                                                                          
               SCOP domains d4hmsa_ A: Pyridoxine 5'-phoshate oxidase (PNP oxidase)                                                                                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh..hhhhhhhhhhhhhhhhh.....eeeeeee.....eeeeeee..ee...eeeeeee..hhhhhhhhhh.eeeeeeee....eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..........eeeeeeeeeeeeeeeeee..eeeeeeeee....eeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hms A  21 GTLDAPFPEYQTLPADPMSVLHNWLERARRVGIREPRALALATADSQGRPSTRIVVISEISDAGVVFSTHAGSQKGRELLHNPWASGVLYWRETSQQIILNGQAVRLPNAKADDAWLKRPYATHPMSSVSRQSEELQDVQAMRNAARQLAELQGPLPRPEGYCVFELRLESLEFWGNGQERLHERLRYDRSDTGWNVRRLQP 222
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  


Chain B from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                              
               SCOP domains d4hmsb_ B: Pyridoxine 5'-phoshate oxidase (PNP oxidase)                                                                                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhh..hhhhhhhhhhhhhhhhh.....eeeeeee.....eeeeeee..ee...eeeeeee..hhhhhhhhhh.eeeeeeee....eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..........eeeeeeeeeeeeeeeeee..eeeeeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hms B  17 ESLTGTLDAPFPEYQTLPADPMSVLHNWLERARRVGIREPRALALATADSQGRPSTRIVVISEISDAGVVFSTHAGSQKGRELLHNPWASGVLYWRETSQQIILNGQAVRLPNAKADDAWLKRPYATHPMSSVSRQSEELQDVQAMRNAARQLAELQGPLPRPEGYCVFELRLESLEFWGNGQERLHERLRYDRSDTGWNVRRLQP 222
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216
   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, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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 ]
    SO4  [ 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 ]
 
  Cis Peptide Bonds
    Gly A:174 - Pro A:175   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  4hms
    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
  PHZG_PSEFL | Q51793
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.4.-.-
    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
  PHZG_PSEFL | Q51793
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PHZG_PSEFL | Q51793: 1ty9 4hmt 4hmu 4hmv

(-) Related Entries Specified in the PDB File

4hmt 4hmu 4hmv 4hmw 4hmx