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 STAPHYLOCOCCAL NUCLEASE VARIANT DELTA+PHS I72R AT CRYOGENIC TEMPERATURE
 
Authors :  M. J. Harms, J. L. Schlessman, E. B. Garcia-Moreno
Date :  23 May 08  (Deposition) - 06 Jan 09  (Release) - 14 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym./Biol. Unit :  A
Keywords :  Staphylococcal Nuclease, Hyperstable Variant, Hydrolase, Internal Arg, Endonuclease, Metal-Binding, Nuclease, Secreted, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. J. Harms, J. L. Schlessman, G. R. Sue, B. Garcia-Moreno E
Arginine Residues At Internal Positions In A Protein Are Always Charged.
Proc. Natl. Acad. Sci. Usa V. 108 18954 2011
PubMed-ID: 22080604  |  Reference-DOI: 10.1073/PNAS.1104808108

(-) Compounds

Molecule 1 - THERMONUCLEASE
    ChainsA
    EC Number3.1.31.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET24A+
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP DATABASE RESIDUES 80-228
    GeneNUC, MW0769
    MutationYES
    Organism ScientificSTAPHYLOCOCCUS AUREUS SUBSP. AUREUS MW2
    Organism Taxid196620
    SynonymTNASE, MICROCOCCAL NUCLEASE, STAPHYLOCOCCAL NUCLEASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2THP1Ligand/IonTHYMIDINE-3',5'-DIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:21 , ASP A:40 , THR A:41 , HOH A:158 , HOH A:204 , HOH A:216BINDING SITE FOR RESIDUE CA A 150
2AC2SOFTWAREARG A:35 , LEU A:37 , ASP A:40 , ASP A:83 , LYS A:84 , TYR A:85 , ARG A:87 , LEU A:89 , TYR A:113 , TYR A:115 , LYS A:127 , HOH A:169 , HOH A:201 , HOH A:203 , HOH A:204 , HOH A:205 , HOH A:211 , HOH A:216BINDING SITE FOR RESIDUE THP A 151

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D8G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3D8G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D8G)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNASE_3PS50830 Thermonuclease domain profile.NUC_STAAW87-221  1A:8-142
2TNASE_1PS01123 Thermonuclease family signature 1.NUC_STAAW98-122  1A:19-43
3TNASE_2PS01284 Thermonuclease family signature 2.NUC_STAAW162-172  1A:83-93

(-) Exons   (0, 0)

(no "Exon" information available for 3D8G)

(-) 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:130
 aligned with NUC_STAAW | Q8NXI6 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:136
                                    95       105       115       125       135       145       155       165       175       185       195       205       215      
            NUC_STAAW    86 LHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFTKKMVENAKKIEVEFDKGQRTDKYGRGLAYIYADGKMVNEALVRQGLAKVAYVYKPNNTHEQLLRKSEAQAKKEKLNIWSE 221
               SCOP domains d3d8ga_ A: Staphylococcal nuclease                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..eeeeee..eeeeee..eeeeeee..ee...------....hhhhhhhhhhhhhhh...eeeee...........eeeeeee..eehhhhhhhh...ee...hhhhh.hhhhhhhhhhhhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -TNASE_3  PDB: A:8-142 UniProt: 87-221                                                                                                   PROSITE (1)
                PROSITE (2) ------------TNASE_1  PDB: A:19-43    ---------------------------------------TNASE_2    ------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d8g A   7 LHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPE------FNEKYGPEASAFTKKMVENAKKREVEFDKGQRTDKYGRGLAYIYADGKMVNEALVRQGLAKVAYVYKGNNTHEQLLRKAEAQAKKEKLNIWSE 142
                                    16        26        36      |  -   |    56        66        76        86        96       106       116       126       136      
                                                               43     50                                                                                            

   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/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3D8G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D8G)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NUC_STAAW | Q8NXI6)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
biological process
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    THP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3d8g)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3d8g
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  NUC_STAAW | Q8NXI6
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.31.1
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  NUC_STAAW | Q8NXI6
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        NUC_STAAW | Q8NXI62gsi 2lkv 2m00 2oxp 2pqe 2pw5 2pw7 2pyk 2pzt 2pzu 2pzw 3d4w 3mvv 3qoj 3qol 3qon 3r3o

(-) Related Entries Specified in the PDB File

3bdc CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT DELTA+ PHS AT CRYOGENIC TEMPERATURE
3d4w CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT DELTA+ PHS A109R AT CRYOGENIC TEMPERATURE