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(-) Description

Title :  CRYOGENIC CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT TRUNCATED DELTA+PHS I92D
 
Authors :  R. L. Reynald, E. E. Lattman, A. G. Gittis
Date :  30 Dec 06  (Deposition) - 25 Mar 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Ob-Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. L. Reynald, R. K. Gitti, E. E. Lattman, A. G. Gittis
Buried Charges And Water In The Protein Interior: Reality Or Fiction?
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - STAPHYLOCOCCAL THERMONUCLEASE
    Chains: A
    EC Number: 3.1.31.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET21A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: NUC
    Mutation: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Strain: FOGGI
    Synonym: TNASE

 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:235 , HOH A:236BINDING SITE FOR RESIDUE CA A 301
2AC2SOFTWAREARG A:35 , LEU A:36 , 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 , HOH A:208 , HOH A:210 , HOH A:212 , HOH A:235 , HOH A:239 , HOH A:241BINDING SITE FOR RESIDUE THP A 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OEO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OEO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OEO)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNASE_3PS50830 Thermonuclease domain profile.NUC_STAAU90-224  1A:8-141
2TNASE_1PS01123 Thermonuclease family signature 1.NUC_STAAU101-125  1A:19-43
3TNASE_2PS01284 Thermonuclease family signature 2.NUC_STAAU165-175  1A:83-93

(-) Exons   (0, 0)

(no "Exon" information available for 2OEO)

(-) 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_STAAU | P00644 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:136
                                    97       107       117       127       137       147       157       167       177       187       197       207       217      
            NUC_STAAU    88 KLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFTKKMVENAKKIEVEFDKGQRTDKYGRGLAYIYADGKMVNEALVRQGLAKVAYVYKPNNTHEQHLRKSEAQAKKEKLNIWS 223
               SCOP domains d2oeoa_ A: Staphylococcal nuclease                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------SNase-2oeoA      01 A:33-141                                                                                  Pfam domains
         Sec.struct. author ....eeeeeeee....eeeeee..eeeeeee..ee...------....hhhhhhhhhhhhhhh...eeeee...........eeeeeee..eehhhhhhhh...ee...hhhhh.hhhhhhhhhhhhhhh.hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --TNASE_3  PDB: A:8-141 UniProt: 90-224                                                                                                  PROSITE (1)
                PROSITE (2) -------------TNASE_1  PDB: A:19-43    ---------------------------------------TNASE_2    ------------------------------------------------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oeo A   6 KLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPE------FNEKYGPEASAFTKAMVENAKKIEVEFDKGQRTDKYGRGLAYDYADGAMVNEALVRQGLAAVAYVYSGNNTHEQLLRAAEAQAKKEKLNIWS 141
                                    15        25        35       | -    |   55        65        75        85        95       105       115       125       135      
                                                                43     50
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2OEO)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: SNase] (72)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NUC_STAAU | P00644)
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.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NUC_STAAU | P00644: 1a2t 1a2u 1a3t 1a3u 1a3v 1aex 1ena 1enc 1eqv 1ey0 1ey4 1ey5 1ey6 1ey7 1ey8 1ey9 1eya 1eyc 1eyd 1ez6 1ez8 1f2m 1f2y 1f2z 1ihz 1ii3 1jok 1joo 1joq 1jor 1kaa 1kab 1kda 1kdb 1kdc 1nsn 1nuc 1rkn 1snc 1snd 1snm 1sno 1snp 1snq 1sta 1stb 1stg 1sth 1stn 1sty 1syb 1syc 1syd 1sye 1syf 1syg 1tqo 1tr5 1tt2 1u9r 2enb 2exz 2ey1 2ey2 2ey5 2ey6 2eyf 2eyh 2eyj 2eyl 2eym 2eyo 2eyp 2f0d 2f0e 2f0f 2f0g 2f0h 2f0i 2f0j 2f0k 2f0l 2f0m 2f0n 2f0o 2f0p 2f0q 2f0s 2f0t 2f0u 2f0v 2f0w 2f3v 2f3w 2fxy 2fxz 2gsi 2khs 2nuc 2of1 2pqe 2qdb 2rbm 2rdf 2rks 2snm 2sns 2sob 3bdc 3c1e 3c1f 3d4d 3d6c 3dhq 3dmu 3e5s 3eji 3ero 3erq 3evq 3h6m 3hej 3hzx 3itp 3lx0 3meh 3mhb 3mvv 3mxp 3mz5 3nhh 3nk9 3np8 3nqt 3nuc 3nxw 3oso 3owf 3p1h 3p75 3pmf 3qb3 3qoj 3qol 3qon 3r3o 3ruz 3s9w 3shl 3sk4 3sk5 3sk6 3sk8 3sr1 3sxh 3t13 3t16 3tme 3tp5 3tp6 3tp7 3tp8 3u9o 3v2t 3va5 4df7 4dfa 4dgz 4du9 4e6i 4eqn 4eqo 4eqp 4evo 4f7x 4f8m 4g57 4h7b 4hmi 4hmj 4hth 4i65 4ial 4id6 4iun 4iz8 4j1m 4j6h 4k14 4k2k 4k2l 4k5v 4k5w 4k5x 4k6d 4k8i 4k8j 4kd3 4kd4 4khv 4kjn 4kjo 4kta 4kv6 4ky5 4ky6 4ky7 4laa 4me5 4miu 4n9p 4n9t 4ndx 4nkl 4nmz 4np5 4odg 4ol7 4pmb 4pmc 4pny 4qb4 4qf4 4r8n 4rkb 4rkl 4s3s 4trd 4wor 4yij 4zq3 4zui 4zuj 5c3w 5c3x 5c4h 5c4z 5c5l 5c5m 5c6a 5cc4 5cgk 5cr3 5cv4 5cv5 5cv6 5cv7 5cv8 5cv9 5dau 5deh 5e1f 5e3f 5egt 5ekk 5ekl 5f2d 5hgt 5hur 5i6w 5i6y 5i9o 5i9p 5igb 5igc 5igd 5ige 5igf 5igg 5iif 5ioc 5iod 5isr 5j1z 5j22 5jav 5job 5k5p 5kee 5kgu 5kix 5kru 5kyi 5kyl 5nuc

(-) Related Entries Specified in the PDB File

1tqo CRYOGENIC CRYSTAL STRUCTURE OF THE SAME PROTEIN WITH DIFFERENT IONIZABLE GROUP (I92E MUTANT) IN THE PROTEIN INTERIOR
1tr5 ROOM-TEMPERATURE STRUCTURE OF THE SAME PROTEIN WITH THE MUTATION I92E
1tt2 CRYOGENIC CRYSTAL STRUCTURE OF THE SAME PROTEIN WITH DIFFERENT IONIZABLE GROUP (I92K MUTANT) IN THE PROTEIN INTERIOR
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