HEADER HYDROLASE 28-MAY-04 1WHB TITLE SOLUTION STRUCTURE OF THE RHODANESE-LIKE DOMAIN IN HUMAN UBIQUITIN TITLE 2 SPECIFIC PROTEASE 8 (UBP8) COMPND MOL_ID: 1; COMPND 2 MOLECULE: KIAA0055; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RHODANESE-LIKE DOMAIN; COMPND 5 SYNONYM: UBIQUITIN SPECIFIC PROTEASE 8, UBP8; COMPND 6 EC: 3.1.2.15; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: KAZUSA CDNA HA01049; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P040119-91; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS DEUBIQUTINATING ENZYME, UBPY, STRUCTURAL GENOMICS, RIKEN STRUCTURAL KEYWDS 2 GENOMICS/PROTEOMICS INITIATIVE, RSGI, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.SAITO,S.KOSHIBA,M.INOUE,T.KIGAWA,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 02-MAR-22 1WHB 1 REMARK SEQADV REVDAT 2 24-FEB-09 1WHB 1 VERSN REVDAT 1 28-NOV-04 1WHB 0 JRNL AUTH K.SAITO,S.KOSHIBA,M.INOUE,T.KIGAWA,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE RHODANESE-LIKE DOMAIN IN HUMAN JRNL TITL 2 UBIQUITIN SPECIFIC PROTEASE 8 (UBP8) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, CNS 1.1 REMARK 3 AUTHORS : BRUKER (XWINNMR), BRUNGER, A.T. (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1WHB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-JUN-04. REMARK 100 THE DEPOSITION ID IS D_1000023581. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM PROTEIN, 20MM D-TRIS-HCL, PH REMARK 210 7.0, 100MM NACL, 1MM D-DTT, 0.02% REMARK 210 NAN3, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20020425, NMRVIEW 5, CNS REMARK 210 1.1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 SER A 3 -48.14 -131.03 REMARK 500 1 LYS A 8 -44.22 -141.72 REMARK 500 1 CYS A 9 143.69 69.47 REMARK 500 1 GLU A 10 -63.86 -126.05 REMARK 500 1 PRO A 74 173.86 -51.44 REMARK 500 1 GLU A 88 -79.00 -97.40 REMARK 500 1 PHE A 96 58.75 -154.06 REMARK 500 1 PHE A 116 -53.42 -131.33 REMARK 500 1 TRP A 118 48.93 -103.41 REMARK 500 1 SER A 120 -48.40 -134.10 REMARK 500 1 LYS A 121 -75.98 -106.41 REMARK 500 1 PRO A 154 178.95 -52.18 REMARK 500 2 SER A 6 -176.11 59.79 REMARK 500 2 GLU A 10 83.31 60.15 REMARK 500 2 LYS A 12 78.56 61.37 REMARK 500 2 ASN A 30 -48.99 -145.00 REMARK 500 2 LEU A 50 -75.81 -61.91 REMARK 500 2 VAL A 55 112.91 -162.93 REMARK 500 2 PRO A 62 90.92 -69.33 REMARK 500 2 PRO A 74 174.33 -52.34 REMARK 500 2 GLU A 88 -73.23 -111.14 REMARK 500 2 ASP A 94 -179.96 -176.80 REMARK 500 2 PHE A 96 71.94 -152.16 REMARK 500 2 PHE A 116 -53.35 -133.47 REMARK 500 2 TRP A 118 -63.10 -99.79 REMARK 500 2 GLU A 119 163.62 61.20 REMARK 500 2 LYS A 121 -46.01 -157.43 REMARK 500 2 TYR A 142 74.76 -119.90 REMARK 500 2 GLN A 144 38.58 -96.14 REMARK 500 2 TYR A 145 30.64 -142.99 REMARK 500 2 ALA A 149 78.15 -105.88 REMARK 500 2 LYS A 150 30.94 -153.56 REMARK 500 3 SER A 3 179.09 60.51 REMARK 500 3 LYS A 8 106.98 60.82 REMARK 500 3 GLU A 10 140.08 63.55 REMARK 500 3 LYS A 29 31.11 -98.59 REMARK 500 3 ARG A 40 176.49 -59.76 REMARK 500 3 ASP A 46 -70.05 -74.06 REMARK 500 3 VAL A 55 111.41 -161.84 REMARK 500 3 PRO A 62 91.56 -69.50 REMARK 500 3 PRO A 74 -167.70 -54.37 REMARK 500 3 GLU A 88 -66.46 -101.46 REMARK 500 3 PHE A 96 32.41 -156.85 REMARK 500 3 GLU A 119 155.60 61.00 REMARK 500 3 SER A 120 79.77 -158.39 REMARK 500 3 TYR A 142 80.56 -150.15 REMARK 500 3 GLN A 144 50.82 -90.52 REMARK 500 3 TYR A 145 30.17 -158.04 REMARK 500 3 SER A 155 -77.52 65.38 REMARK 500 4 SER A 2 -78.83 64.45 REMARK 500 REMARK 500 THIS ENTRY HAS 327 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSK002000052.1 RELATED DB: TARGETDB DBREF 1WHB A 8 151 UNP P40818 UBP8_HUMAN 176 319 SEQADV 1WHB GLY A 1 UNP P40818 CLONING ARTIFACT SEQADV 1WHB SER A 2 UNP P40818 CLONING ARTIFACT SEQADV 1WHB SER A 3 UNP P40818 CLONING ARTIFACT SEQADV 1WHB GLY A 4 UNP P40818 CLONING ARTIFACT SEQADV 1WHB SER A 5 UNP P40818 CLONING ARTIFACT SEQADV 1WHB SER A 6 UNP P40818 CLONING ARTIFACT SEQADV 1WHB GLY A 7 UNP P40818 CLONING ARTIFACT SEQADV 1WHB SER A 152 UNP P40818 CLONING ARTIFACT SEQADV 1WHB GLY A 153 UNP P40818 CLONING ARTIFACT SEQADV 1WHB PRO A 154 UNP P40818 CLONING ARTIFACT SEQADV 1WHB SER A 155 UNP P40818 CLONING ARTIFACT SEQADV 1WHB SER A 156 UNP P40818 CLONING ARTIFACT SEQADV 1WHB GLY A 157 UNP P40818 CLONING ARTIFACT SEQRES 1 A 157 GLY SER SER GLY SER SER GLY LYS CYS GLU THR LYS GLU SEQRES 2 A 157 LYS GLY ALA ILE THR ALA LYS GLU LEU TYR THR MET MET SEQRES 3 A 157 THR ASP LYS ASN ILE SER LEU ILE ILE MET ASP ALA ARG SEQRES 4 A 157 ARG MET GLN ASP TYR GLN ASP SER CYS ILE LEU HIS SER SEQRES 5 A 157 LEU SER VAL PRO GLU GLU ALA ILE SER PRO GLY VAL THR SEQRES 6 A 157 ALA SER TRP ILE GLU ALA HIS LEU PRO ASP ASP SER LYS SEQRES 7 A 157 ASP THR TRP LYS LYS ARG GLY ASN VAL GLU TYR VAL VAL SEQRES 8 A 157 LEU LEU ASP TRP PHE SER SER ALA LYS ASP LEU GLN ILE SEQRES 9 A 157 GLY THR THR LEU ARG SER LEU LYS ASP ALA LEU PHE LYS SEQRES 10 A 157 TRP GLU SER LYS THR VAL LEU ARG ASN GLU PRO LEU VAL SEQRES 11 A 157 LEU GLU GLY GLY TYR GLU ASN TRP LEU LEU CYS TYR PRO SEQRES 12 A 157 GLN TYR THR THR ASN ALA LYS VAL SER GLY PRO SER SER SEQRES 13 A 157 GLY HELIX 1 1 THR A 18 THR A 27 1 10 HELIX 2 2 ARG A 40 SER A 47 1 8 HELIX 3 3 THR A 65 HIS A 72 1 8 HELIX 4 4 ASP A 76 LYS A 83 1 8 HELIX 5 5 ARG A 84 ASN A 86 5 3 HELIX 6 6 SER A 98 LEU A 102 5 5 HELIX 7 7 THR A 106 ALA A 114 1 9 HELIX 8 8 GLY A 134 TYR A 142 1 9 HELIX 9 9 PRO A 143 THR A 146 5 4 SHEET 1 A 5 ALA A 16 ILE A 17 0 SHEET 2 A 5 LEU A 129 LEU A 131 1 O VAL A 130 N ILE A 17 SHEET 3 A 5 TYR A 89 LEU A 93 1 N LEU A 92 O LEU A 129 SHEET 4 A 5 LEU A 33 ALA A 38 1 N ILE A 34 O VAL A 91 SHEET 5 A 5 LEU A 53 VAL A 55 1 O LEU A 53 N ILE A 35 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1