HEADER LIGASE 25-OCT-16 5TR5 TITLE SOLUTION STRUCTURE OF SERINE 65 PHOSPHORYLATED UBL DOMAIN FROM PARKIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE PARKIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-76; COMPND 5 SYNONYM: PARKIN,PARKINSON JUVENILE DISEASE PROTEIN 2,PARKINSON COMPND 6 DISEASE PROTEIN 2; COMPND 7 EC: 6.3.2.-; COMPND 8 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: PARK2, PRKN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET SUMO KEYWDS PHOSPHORYLATION, PINK1, PARKINSON'S DISEASE, LIGASE EXPDTA SOLUTION NMR NUMMDL 25 AUTHOR J.D.AGUIRRE,K.M.DUNKERLEY,P.MERCIER,G.S.SHAW REVDAT 5 14-JUN-23 5TR5 1 REMARK REVDAT 4 08-JAN-20 5TR5 1 COMPND REVDAT 3 25-JAN-17 5TR5 1 JRNL REVDAT 2 04-JAN-17 5TR5 1 JRNL REVDAT 1 21-DEC-16 5TR5 0 JRNL AUTH J.D.AGUIRRE,K.M.DUNKERLEY,P.MERCIER,G.S.SHAW JRNL TITL STRUCTURE OF PHOSPHORYLATED UBL DOMAIN AND INSIGHTS INTO JRNL TITL 2 PINK1-ORCHESTRATED PARKIN ACTIVATION. JRNL REF PROC. NATL. ACAD. SCI. V. 114 298 2017 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 28007983 JRNL DOI 10.1073/PNAS.1613040114 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5TR5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1000223018. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 300 UM [U-15N] PUBL, 25 MM REMARK 210 HEPES, 100 MM SODIUM CHLORIDE, REMARK 210 250 UM TCEP, 200 UM DSS, 300 UM REMARK 210 IMIDAZOLE, 90% H2O/10% D2O; 300 REMARK 210 UM [U-13C] PUBL, 25 MM HEPES, REMARK 210 100 MM SODIUM CHLORIDE, 250 UM REMARK 210 TCEP, 200 UM DSS, 300 UM REMARK 210 IMIDAZOLE, 90% H2O/10% D2O; 400 REMARK 210 UM [U-99% 13C; U-99% 15N] PUBL, REMARK 210 25 MM HEPES, 100 MM SODIUM REMARK 210 CHLORIDE, 250 UM TCEP, 200 UM REMARK 210 DSS, 300 UM IMIDAZOLE, 90% H2O/ REMARK 210 10% D2O; 400 UM PUBL, 25 MM REMARK 210 HEPES, 100 MM SODIUM CHLORIDE, REMARK 210 250 UM TCEP, 200 UM DSS, 300 UM REMARK 210 IMIDAZOLE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HNCA; 3D HNCACB; 3D REMARK 210 HNCO; 3D C(CO)NH; 3D HCCH-TOCSY; REMARK 210 2D (HB)CB(CGCD)HD; 3D 1H-13C REMARK 210 NOESY ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D 1H-15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 8.9, NMRVIEW 8.2.4, VNMR REMARK 210 3.2, CYANA REMARK 210 METHOD USED : NA REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 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: 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 THR A 55 HG CYS A 59 1.60 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 HIS A 11 -166.14 -105.38 REMARK 500 1 SEP A 65 -151.86 59.24 REMARK 500 2 SEP A 65 -158.30 53.64 REMARK 500 3 ASN A 8 23.11 45.96 REMARK 500 3 HIS A 11 179.14 66.79 REMARK 500 3 ASP A 53 70.74 -110.71 REMARK 500 3 SEP A 65 -104.39 55.07 REMARK 500 4 HIS A 11 -169.34 -110.85 REMARK 500 4 ASP A 60 91.01 60.34 REMARK 500 4 GLN A 64 -159.67 -84.18 REMARK 500 5 HIS A 11 -157.20 -103.09 REMARK 500 5 GLN A 64 -156.10 -95.62 REMARK 500 5 SEP A 65 -170.41 -66.79 REMARK 500 6 ASP A 60 80.61 63.53 REMARK 500 6 SEP A 65 164.09 80.04 REMARK 500 7 SER A 9 14.63 55.31 REMARK 500 7 SER A 10 -68.77 -90.41 REMARK 500 7 ASP A 60 71.95 58.76 REMARK 500 7 ARG A 75 32.16 -140.59 REMARK 500 8 GLN A 64 -154.78 -120.15 REMARK 500 8 ARG A 75 81.02 57.71 REMARK 500 9 SER A 10 -152.49 -87.16 REMARK 500 9 ALA A 46 -63.58 68.46 REMARK 500 10 GLN A 64 -84.17 -68.47 REMARK 500 11 HIS A 11 -79.89 64.37 REMARK 500 11 ASP A 53 73.01 -102.62 REMARK 500 11 GLN A 64 -160.39 -78.46 REMARK 500 12 HIS A 11 -74.29 -94.50 REMARK 500 12 GLN A 64 -71.46 -128.03 REMARK 500 12 PRO A 73 94.79 -67.17 REMARK 500 13 SER A 10 -146.24 -92.55 REMARK 500 13 ASP A 53 79.68 -113.50 REMARK 500 14 GLN A 64 -76.40 -92.84 REMARK 500 15 SER A 10 -79.21 -67.01 REMARK 500 15 HIS A 11 -58.62 -132.43 REMARK 500 15 ASP A 20 69.24 -101.03 REMARK 500 15 ALA A 46 -66.25 68.66 REMARK 500 15 ASP A 53 74.36 -102.84 REMARK 500 15 GLN A 64 -165.72 -75.39 REMARK 500 16 SER A 10 -158.80 -88.99 REMARK 500 16 ASP A 60 50.41 -69.41 REMARK 500 16 GLN A 64 -155.99 -102.40 REMARK 500 16 SEP A 65 -163.39 -71.52 REMARK 500 16 ARG A 75 76.33 56.80 REMARK 500 17 ASN A 8 -44.83 66.70 REMARK 500 17 SEP A 65 -168.18 57.43 REMARK 500 18 SER A 10 -162.96 -121.43 REMARK 500 18 SEP A 65 -164.74 62.61 REMARK 500 19 ALA A 46 -62.46 68.18 REMARK 500 19 ASP A 53 79.12 -103.83 REMARK 500 REMARK 500 THIS ENTRY HAS 73 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30197 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF SERINE 65 PHOSPHORYLATED UBL DOMAIN FROM REMARK 900 PARKIN DBREF 5TR5 A 1 76 UNP O60260 PRKN2_HUMAN 1 76 SEQRES 1 A 76 MET ILE VAL PHE VAL ARG PHE ASN SER SER HIS GLY PHE SEQRES 2 A 76 PRO VAL GLU VAL ASP SER ASP THR SER ILE PHE GLN LEU SEQRES 3 A 76 LYS GLU VAL VAL ALA LYS ARG GLN GLY VAL PRO ALA ASP SEQRES 4 A 76 GLN LEU ARG VAL ILE PHE ALA GLY LYS GLU LEU ARG ASN SEQRES 5 A 76 ASP TRP THR VAL GLN ASN CYS ASP LEU ASP GLN GLN SEP SEQRES 6 A 76 ILE VAL HIS ILE VAL GLN ARG PRO TRP ARG LYS MODRES 5TR5 SEP A 65 SER MODIFIED RESIDUE HET SEP A 65 14 HETNAM SEP PHOSPHOSERINE HETSYN SEP PHOSPHONOSERINE FORMUL 1 SEP C3 H8 N O6 P HELIX 1 AA1 ILE A 23 GLN A 34 1 12 HELIX 2 AA2 VAL A 56 CYS A 59 1 4 HELIX 3 AA3 LEU A 61 GLN A 64 1 4 SHEET 1 AA1 4 MET A 1 ARG A 6 0 SHEET 2 AA1 4 PHE A 13 VAL A 17 0 SHEET 3 AA1 4 LEU A 41 ILE A 44 1 O VAL A 67 N ARG A 6 SHEET 4 AA1 4 VAL A 67 GLN A 71 0 LINK C GLN A 64 N SEP A 65 1555 1555 1.33 LINK C SEP A 65 N ILE A 66 1555 1555 1.32 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