PDB Short entry for 1MG8 HEADER APOPTOSIS 15-AUG-02 1MG8 TITLE NMR STRUCTURE OF UBIQUITIN-LIKE DOMAIN IN MURINE PARKIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PARKIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UBIQUITIN-LIKE DOMAIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 STRAIN: BL21 (DE3); SOURCE 6 PLASMID: PET28B KEYWDS PARKINSON DISEASE, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, KEYWDS 2 RSGI, STRUCTURAL GENOMICS, APOPTOSIS EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.TASHIRO,S.OKUBO,S.SHIMOTAKAHARA,H.HATANAKA,H.YASUDA,M.KAINOSHO, AUTHOR 2 S.YOKOYAMA,H.SHINDO,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE AUTHOR 3 (RSGI) REVDAT 4 21-DEC-22 1MG8 1 SEQADV REVDAT 3 23-FEB-22 1MG8 1 REMARK SEQADV REVDAT 2 24-FEB-09 1MG8 1 VERSN REVDAT 1 08-APR-03 1MG8 0 JRNL AUTH M.TASHIRO,S.OKUBO,S.SHIMOTAKAHARA,H.HATANAKA,H.YASUDA, JRNL AUTH 2 M.KAINOSHO,S.YOKOYAMA,H.SHINDO JRNL TITL NMR STRUCTURE OF UBIQUITIN-LIKE DOMAIN IN PARKIN: GENE JRNL TITL 2 PRODUCT OF FAMILIAL PARKINSON'S DISEASE. JRNL REF J.BIOMOL.NMR V. 25 153 2003 JRNL REFN ISSN 0925-2738 JRNL PMID 12652124 JRNL DOI 10.1023/A:1022254432039 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.KITADA,S.ASAKAWA,N.HATTORI,H.MATSUMINE,Y.YAMAMURA, REMARK 1 AUTH 2 S.MINOSIMA,M.YOKOCHI,Y.MIZUNO,N.SHIMIZU REMARK 1 TITL MUTATIONS IN THE PARKIN GENE CAUSES AUTOSOMAL RECESSIVE REMARK 1 TITL 2 JUVENILE PARKINSONISM REMARK 1 REF NATURE V. 392 605 1998 REMARK 1 REFN ISSN 0028-0836 REMARK 1 DOI 10.1038/33416 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1MG8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-AUG-02. REMARK 100 THE DEPOSITION ID IS D_1000016892. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM UBIQUITIN-LIKE DOMAIN U REMARK 210 -15N,13C; 25MM ACETATE BUFFER NA, REMARK 210 2MM DITHIOTHREITOL-D10 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX; DRX; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY. 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 9 PHE A 9 CB - CG - CD2 ANGL. DEV. = -5.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 PHE A 9 96.64 -68.89 REMARK 500 1 ASN A 10 -131.31 61.61 REMARK 500 1 SER A 12 -1.43 77.60 REMARK 500 1 SER A 24 -142.40 -60.84 REMARK 500 1 ILE A 25 -31.11 -130.17 REMARK 500 1 ALA A 48 7.76 59.61 REMARK 500 1 ASP A 62 30.63 103.78 REMARK 500 1 GLU A 64 152.41 59.96 REMARK 500 1 GLN A 66 106.40 74.60 REMARK 500 1 SER A 67 130.38 -171.81 REMARK 500 1 ARG A 74 96.95 -39.57 REMARK 500 1 ARG A 77 92.98 -54.12 REMARK 500 2 ASN A 10 -90.78 62.12 REMARK 500 2 SER A 11 -71.12 -128.35 REMARK 500 2 SER A 24 -142.61 -61.24 REMARK 500 2 ASP A 62 36.61 155.02 REMARK 500 2 GLU A 64 -154.34 46.99 REMARK 500 2 GLN A 66 109.35 74.39 REMARK 500 2 SER A 67 129.84 -175.87 REMARK 500 2 ARG A 74 108.35 -53.64 REMARK 500 2 ARG A 77 92.28 -53.70 REMARK 500 3 ASN A 10 162.99 54.46 REMARK 500 3 SER A 11 -109.21 34.89 REMARK 500 3 TYR A 13 153.74 -48.12 REMARK 500 3 SER A 24 -142.81 69.31 REMARK 500 3 ILE A 25 -25.50 -144.15 REMARK 500 3 ASP A 62 32.77 109.13 REMARK 500 3 GLU A 64 -157.51 51.60 REMARK 500 3 GLN A 66 111.54 80.23 REMARK 500 3 SER A 67 129.72 -173.34 REMARK 500 3 ARG A 77 90.79 -55.90 REMARK 500 4 ASN A 10 -91.04 61.62 REMARK 500 4 SER A 11 -63.76 -165.30 REMARK 500 4 TYR A 13 -160.92 -105.30 REMARK 500 4 ILE A 25 -30.57 72.35 REMARK 500 4 ALA A 48 7.74 55.66 REMARK 500 4 ASP A 62 37.45 103.26 REMARK 500 4 LEU A 63 -83.23 -66.60 REMARK 500 4 GLU A 64 162.26 76.45 REMARK 500 4 GLN A 66 112.30 76.00 REMARK 500 4 SER A 67 118.58 -163.18 REMARK 500 4 ARG A 74 105.02 -48.24 REMARK 500 4 ARG A 77 92.33 -56.42 REMARK 500 5 ASN A 10 -84.62 68.18 REMARK 500 5 SER A 11 -32.09 -177.20 REMARK 500 5 SER A 24 -144.53 65.78 REMARK 500 5 ILE A 25 -28.26 -144.94 REMARK 500 5 GLU A 51 88.75 -48.36 REMARK 500 5 LEU A 56 162.74 -42.47 REMARK 500 5 ASP A 62 36.07 105.56 REMARK 500 REMARK 500 THIS ENTRY HAS 104 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 8 0.31 SIDE CHAIN REMARK 500 1 ARG A 74 0.22 SIDE CHAIN REMARK 500 1 ARG A 76 0.28 SIDE CHAIN REMARK 500 1 ARG A 77 0.27 SIDE CHAIN REMARK 500 1 ARG A 78 0.24 SIDE CHAIN REMARK 500 2 ARG A 8 0.17 SIDE CHAIN REMARK 500 2 ARG A 35 0.30 SIDE CHAIN REMARK 500 2 ARG A 44 0.13 SIDE CHAIN REMARK 500 2 ARG A 74 0.28 SIDE CHAIN REMARK 500 2 ARG A 76 0.14 SIDE CHAIN REMARK 500 2 ARG A 77 0.29 SIDE CHAIN REMARK 500 2 ARG A 78 0.23 SIDE CHAIN REMARK 500 3 ARG A 8 0.29 SIDE CHAIN REMARK 500 3 ARG A 35 0.30 SIDE CHAIN REMARK 500 3 ARG A 44 0.30 SIDE CHAIN REMARK 500 3 ARG A 74 0.16 SIDE CHAIN REMARK 500 3 ARG A 76 0.14 SIDE CHAIN REMARK 500 3 ARG A 77 0.22 SIDE CHAIN REMARK 500 3 ARG A 78 0.31 SIDE CHAIN REMARK 500 4 ARG A 8 0.31 SIDE CHAIN REMARK 500 4 ARG A 35 0.31 SIDE CHAIN REMARK 500 4 ARG A 44 0.32 SIDE CHAIN REMARK 500 4 ARG A 74 0.30 SIDE CHAIN REMARK 500 4 ARG A 76 0.24 SIDE CHAIN REMARK 500 4 ARG A 77 0.32 SIDE CHAIN REMARK 500 4 ARG A 78 0.31 SIDE CHAIN REMARK 500 5 ARG A 8 0.32 SIDE CHAIN REMARK 500 5 ARG A 35 0.17 SIDE CHAIN REMARK 500 5 ARG A 44 0.30 SIDE CHAIN REMARK 500 5 ARG A 74 0.28 SIDE CHAIN REMARK 500 5 ARG A 76 0.30 SIDE CHAIN REMARK 500 5 ARG A 77 0.32 SIDE CHAIN REMARK 500 5 ARG A 78 0.28 SIDE CHAIN REMARK 500 6 ARG A 8 0.28 SIDE CHAIN REMARK 500 6 ARG A 35 0.30 SIDE CHAIN REMARK 500 6 ARG A 44 0.23 SIDE CHAIN REMARK 500 6 ARG A 74 0.31 SIDE CHAIN REMARK 500 6 ARG A 76 0.31 SIDE CHAIN REMARK 500 6 ARG A 77 0.21 SIDE CHAIN REMARK 500 6 ARG A 78 0.29 SIDE CHAIN REMARK 500 7 ARG A 8 0.29 SIDE CHAIN REMARK 500 7 ARG A 35 0.30 SIDE CHAIN REMARK 500 7 ARG A 44 0.31 SIDE CHAIN REMARK 500 7 ARG A 74 0.30 SIDE CHAIN REMARK 500 7 ARG A 76 0.14 SIDE CHAIN REMARK 500 7 ARG A 77 0.32 SIDE CHAIN REMARK 500 8 ARG A 8 0.27 SIDE CHAIN REMARK 500 8 ARG A 35 0.30 SIDE CHAIN REMARK 500 8 ARG A 44 0.23 SIDE CHAIN REMARK 500 8 ARG A 74 0.26 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 67 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: TRT001000160.1 RELATED DB: TARGETDB DBREF 1MG8 A 3 78 UNP Q9WVS6 PRKN2_MOUSE 1 76 SEQADV 1MG8 MET A 1 UNP Q9WVS6 INITIATING METHIONINE SEQADV 1MG8 GLY A 2 UNP Q9WVS6 CLONING ARTIFACT SEQRES 1 A 78 MET GLY MET ILE VAL PHE VAL ARG PHE ASN SER SER TYR SEQRES 2 A 78 GLY PHE PRO VAL GLU VAL ASP SER ASP THR SER ILE LEU SEQRES 3 A 78 GLN LEU LYS GLU VAL VAL ALA LYS ARG GLN GLY VAL PRO SEQRES 4 A 78 ALA ASP GLN LEU ARG VAL ILE PHE ALA GLY LYS GLU LEU SEQRES 5 A 78 PRO ASN HIS LEU THR VAL GLN ASN CYS ASP LEU GLU GLN SEQRES 6 A 78 GLN SER ILE VAL HIS ILE VAL GLN ARG PRO ARG ARG ARG HELIX 1 1 ILE A 25 GLY A 37 1 13 SHEET 1 A 4 GLY A 14 GLU A 18 0 SHEET 2 A 4 ILE A 4 ARG A 8 -1 N VAL A 5 O VAL A 17 SHEET 3 A 4 ILE A 68 ILE A 71 1 O VAL A 69 N PHE A 6 SHEET 4 A 4 VAL A 45 PHE A 47 -1 N ILE A 46 O HIS A 70 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