HEADER LIGASE 13-AUG-02 1IYF TITLE SOLUTION STRUCTURE OF UBIQUITIN-LIKE DOMAIN OF HUMAN PARKIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PARKIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UBIQUITIN-LIKE DOMAIN; COMPND 5 EC: 6.3.2.19; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)CODONPLUS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX6P3 KEYWDS UBIQUITIN FOLD, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, KEYWDS 2 RSGI, STRUCTURAL GENOMICS, LIGASE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR E.SAKATA,Y.YAMAGUCHI,E.KURIMOTO,J.KIKUCHI,S.YOKOYAMA,H.KAWAHARA, AUTHOR 2 H.YOKOSAWA,N.HATTORI,Y.MIZUNO,K.TANAKA,K.KATO,RIKEN STRUCTURAL AUTHOR 3 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 27-DEC-23 1IYF 1 REMARK REVDAT 3 23-FEB-22 1IYF 1 REMARK SEQADV REVDAT 2 24-FEB-09 1IYF 1 VERSN REVDAT 1 25-MAR-03 1IYF 0 JRNL AUTH E.SAKATA,Y.YAMAGUCHI,E.KURIMOTO,J.KIKUCHI,S.YOKOYAMA, JRNL AUTH 2 S.YAMADA,H.KAWAHARA,H.YOKOSAWA,N.HATTORI,Y.MIZUNO,K.TANAKA, JRNL AUTH 3 K.KATO JRNL TITL PARKIN BINDS THE RPN10 SUBUNIT OF 26S PROTEASOMES THROUGH JRNL TITL 2 ITS UBIQUITIN-LIKE DOMAIN JRNL REF EMBO REP. V. 4 301 2003 JRNL REFN ISSN 1469-221X JRNL PMID 12634850 JRNL DOI 10.1038/SJ.EMBOR.EMBOR764 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, CNS 1.1 REMARK 3 AUTHORS : BRUNGER (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 720 RESTRAINTS, 489 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 82 REMARK 3 DIHEDRAL ANGLE RESTRAINTS, 129 RESIDUAL DIPOLAR COUPLING REMARK 3 CONSTRAINTS, 20 DISTANCE RESTRAINTS FOR HYDROGEN BONDS. REMARK 4 REMARK 4 1IYF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-AUG-02. REMARK 100 THE DEPOSITION ID IS D_1000005405. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303; 310 REMARK 210 PH : 6.0; 6.0 REMARK 210 IONIC STRENGTH : 0.3; 0.3 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 0.1MM PARKIN UBIQUITIN-LIKE REMARK 210 DOMAIN U-15N, 13C; 50MM REMARK 210 POTASSIUM PHOSPHATE BUFFER; REMARK 210 0.1MM PARKIN UBIQUITIN-LIKE REMARK 210 DOMAIN U-15N, 13C; 50MM REMARK 210 POTASSIUM PHOSPHATE BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 2D_1H-COUPLED_ REMARK 210 1H-15N_HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.6, CNS 1.1 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 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 : 1 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 GLY A -4 REMARK 465 PRO A -3 REMARK 465 LEU A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O PHE A 7 H SER A 9 1.55 REMARK 500 O ILE A 44 O HIS A 68 2.10 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 ASN A 8 69.22 -63.01 REMARK 500 1 HIS A 11 115.51 -160.52 REMARK 500 1 VAL A 17 154.60 177.10 REMARK 500 1 THR A 21 154.39 -37.18 REMARK 500 1 SER A 22 142.73 -18.26 REMARK 500 1 ILE A 23 -39.43 -39.70 REMARK 500 1 VAL A 30 -71.78 -58.46 REMARK 500 1 PRO A 37 -152.24 -65.17 REMARK 500 1 ALA A 38 -70.44 -106.54 REMARK 500 1 LEU A 41 -143.33 -82.67 REMARK 500 1 ALA A 46 36.28 23.62 REMARK 500 1 LEU A 50 87.81 -9.77 REMARK 500 1 VAL A 56 -133.45 -70.66 REMARK 500 1 CYS A 59 -78.66 -81.36 REMARK 500 1 ASP A 60 76.02 -168.73 REMARK 500 2 ASN A 8 68.90 -63.73 REMARK 500 2 VAL A 17 152.40 178.88 REMARK 500 2 THR A 21 150.58 -33.51 REMARK 500 2 SER A 22 142.99 -17.30 REMARK 500 2 ILE A 23 -39.99 -39.69 REMARK 500 2 VAL A 30 -73.41 -58.78 REMARK 500 2 PRO A 37 -148.87 -66.30 REMARK 500 2 ALA A 38 -68.02 -105.31 REMARK 500 2 GLN A 40 -76.31 -53.20 REMARK 500 2 LEU A 41 -138.36 -84.74 REMARK 500 2 ALA A 46 34.90 26.03 REMARK 500 2 LEU A 50 89.51 -14.52 REMARK 500 2 VAL A 56 -133.53 -82.29 REMARK 500 2 CYS A 59 -76.99 -96.71 REMARK 500 2 ASP A 60 76.65 -169.94 REMARK 500 3 ASN A 8 69.39 -63.91 REMARK 500 3 VAL A 17 157.59 175.41 REMARK 500 3 THR A 21 153.69 -35.19 REMARK 500 3 SER A 22 144.27 -16.62 REMARK 500 3 VAL A 30 -73.53 -61.88 REMARK 500 3 PRO A 37 -147.57 -67.04 REMARK 500 3 ALA A 38 -69.82 -105.96 REMARK 500 3 GLN A 40 -77.32 -49.02 REMARK 500 3 LEU A 41 -124.71 -81.94 REMARK 500 3 ALA A 46 37.86 26.87 REMARK 500 3 LEU A 50 107.64 -25.05 REMARK 500 3 VAL A 56 -135.01 -82.26 REMARK 500 3 CYS A 59 -79.10 -106.22 REMARK 500 3 ASP A 60 76.46 -165.39 REMARK 500 4 ASN A 8 68.53 -64.13 REMARK 500 4 VAL A 17 154.71 178.99 REMARK 500 4 THR A 21 152.42 -34.35 REMARK 500 4 SER A 22 143.14 -18.87 REMARK 500 4 VAL A 30 -74.01 -59.05 REMARK 500 4 PRO A 37 -145.19 -68.20 REMARK 500 REMARK 500 THIS ENTRY HAS 149 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5500 RELATED DB: BMRB REMARK 900 5500 IS CHEMICAL SHIFT REMARK 900 RELATED ID: MY_001000012.1 RELATED DB: TARGETDB DBREF 1IYF A 1 76 UNP O60260 PRKN2_HUMAN 1 76 SEQADV 1IYF GLY A -4 UNP O60260 CLONING ARTIFACT SEQADV 1IYF PRO A -3 UNP O60260 CLONING ARTIFACT SEQADV 1IYF LEU A -2 UNP O60260 CLONING ARTIFACT SEQADV 1IYF GLY A -1 UNP O60260 CLONING ARTIFACT SEQADV 1IYF SER A 0 UNP O60260 CLONING ARTIFACT SEQRES 1 A 81 GLY PRO LEU GLY SER MET ILE VAL PHE VAL ARG PHE ASN SEQRES 2 A 81 SER SER HIS GLY PHE PRO VAL GLU VAL ASP SER ASP THR SEQRES 3 A 81 SER ILE PHE GLN LEU LYS GLU VAL VAL ALA LYS ARG GLN SEQRES 4 A 81 GLY VAL PRO ALA ASP GLN LEU ARG VAL ILE PHE ALA GLY SEQRES 5 A 81 LYS GLU LEU ARG ASN ASP TRP THR VAL GLN ASN CYS ASP SEQRES 6 A 81 LEU ASP GLN GLN SER ILE VAL HIS ILE VAL GLN ARG PRO SEQRES 7 A 81 TRP ARG LYS HELIX 1 1 SER A 22 GLN A 34 1 13 HELIX 2 2 VAL A 56 LEU A 61 1 6 SHEET 1 A 5 HIS A 11 VAL A 15 0 SHEET 2 A 5 ILE A 2 PHE A 7 -1 N VAL A 5 O PHE A 13 SHEET 3 A 5 GLN A 64 VAL A 70 1 O ILE A 69 N ARG A 6 SHEET 4 A 5 ARG A 42 PHE A 45 -1 N ARG A 42 O VAL A 70 SHEET 5 A 5 LYS A 48 GLU A 49 -1 O LYS A 48 N PHE A 45 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