PDB Short entry for 5C9V HEADER SIGNALING PROTEIN 29-JUN-15 5C9V TITLE STRUCTURE OF HUMAN PARKIN G319A COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE PARKIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 137-465; 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; COMPND 9 MUTATION: YES; COMPND 10 OTHER_DETAILS: ENGINEERED MUTATION AT POSITION G319A 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 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: POPINK KEYWDS PARKIN, UBIQUITIN, E3 LIGASE, RBR, PARKINSON'S DISEASE, MITOPHAGY, KEYWDS 2 CELL SIGNALLING, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.WAUER,D.KOMANDER REVDAT 5 10-JAN-24 5C9V 1 REMARK REVDAT 4 13-SEP-17 5C9V 1 REMARK REVDAT 3 26-AUG-15 5C9V 1 JRNL REVDAT 2 29-JUL-15 5C9V 1 JRNL REVDAT 1 22-JUL-15 5C9V 0 JRNL AUTH T.WAUER,M.SIMICEK,A.SCHUBERT,D.KOMANDER JRNL TITL MECHANISM OF PHOSPHO-UBIQUITIN-INDUCED PARKIN ACTIVATION. JRNL REF NATURE V. 524 370 2015 JRNL REFN ESSN 1476-4687 JRNL PMID 26161729 JRNL DOI 10.1038/NATURE14879 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.WAUER,D.KOMANDER REMARK 1 TITL STRUCTURE OF THE HUMAN PARKIN LIGASE DOMAIN IN AN REMARK 1 TITL 2 AUTOINHIBITED STATE. REMARK 1 REF EMBO J. V. 32 2099 2013 REMARK 1 REFN ESSN 1460-2075 REMARK 1 PMID 23727886 REMARK 1 DOI 10.1038/EMBOJ.2013.125 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 84.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 22270 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.150 REMARK 3 FREE R VALUE TEST SET COUNT : 1148 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 84.7350 - 4.6998 1.00 2724 143 0.1701 0.1904 REMARK 3 2 4.6998 - 3.7304 1.00 2681 131 0.1585 0.2267 REMARK 3 3 3.7304 - 3.2588 1.00 2616 147 0.1981 0.2167 REMARK 3 4 3.2588 - 2.9608 1.00 2634 148 0.2282 0.2211 REMARK 3 5 2.9608 - 2.7486 1.00 2641 132 0.2522 0.2630 REMARK 3 6 2.7486 - 2.5865 1.00 2638 137 0.2528 0.2808 REMARK 3 7 2.5865 - 2.4570 1.00 2590 158 0.2624 0.3119 REMARK 3 8 2.4570 - 2.3500 1.00 2598 152 0.2722 0.2852 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 2450 REMARK 3 ANGLE : 0.691 3324 REMARK 3 CHIRALITY : 0.029 346 REMARK 3 PLANARITY : 0.003 432 REMARK 3 DIHEDRAL : 13.913 872 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 7.8845 31.4194 36.9402 REMARK 3 T TENSOR REMARK 3 T11: 0.3663 T22: 0.3066 REMARK 3 T33: 0.2457 T12: -0.0140 REMARK 3 T13: 0.0139 T23: 0.0305 REMARK 3 L TENSOR REMARK 3 L11: 4.1353 L22: 1.2053 REMARK 3 L33: 0.6839 L12: 1.1426 REMARK 3 L13: 0.0605 L23: -0.1762 REMARK 3 S TENSOR REMARK 3 S11: -0.0275 S12: 0.2777 S13: -0.0836 REMARK 3 S21: 0.0212 S22: 0.0596 S23: -0.0111 REMARK 3 S31: -0.0069 S32: 0.0155 S33: -0.0337 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5C9V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000211277. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91730 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22270 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 86.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.80000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 4BM9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 M LITHIUM SULPHATE, 0.01 M MGCL2, REMARK 280 0.05 M MES PH 5.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 84.68000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 48.89002 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 32.33000 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 84.68000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 48.89002 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 32.33000 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 84.68000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 48.89002 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 32.33000 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 84.68000 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 48.89002 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 32.33000 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 84.68000 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 48.89002 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 32.33000 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 84.68000 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 48.89002 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 32.33000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 97.78004 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 64.66000 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 97.78004 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 64.66000 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 97.78004 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 64.66000 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 97.78004 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 64.66000 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 97.78004 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 64.66000 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 97.78004 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 64.66000 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 KCAL/MOL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 S SO4 A 510 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 601 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 632 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 680 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 136 REMARK 465 PRO A 137 REMARK 465 ALA A 138 REMARK 465 GLY A 139 REMARK 465 ARG A 140 REMARK 465 SER A 141 REMARK 465 GLY A 354 REMARK 465 GLY A 355 REMARK 465 ASN A 356 REMARK 465 GLY A 385 REMARK 465 THR A 386 REMARK 465 THR A 387 REMARK 465 THR A 388 REMARK 465 GLN A 389 REMARK 465 ALA A 390 REMARK 465 ALA A 405 REMARK 465 ALA A 406 REMARK 465 SER A 407 REMARK 465 LYS A 408 REMARK 465 GLU A 409 REMARK 465 THR A 410 REMARK 465 ILE A 411 REMARK 465 LYS A 412 REMARK 465 LYS A 413 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ILE A 142 CG1 CG2 CD1 REMARK 470 GLU A 195 CG CD OE1 OE2 REMARK 470 ARG A 234 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 282 CG CD OE1 NE2 REMARK 470 LEU A 283 CG CD1 CD2 REMARK 470 GLU A 310 CG CD OE1 OE2 REMARK 470 GLU A 344 CG CD OE1 OE2 REMARK 470 ASP A 346 CG OD1 OD2 REMARK 470 GLN A 347 CG CD OE1 NE2 REMARK 470 LEU A 358 CG CD1 CD2 REMARK 470 GLU A 374 CG CD OE1 OE2 REMARK 470 ARG A 392 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 399 CG CD OE1 OE2 REMARK 470 GLU A 426 CG CD OE1 OE2 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 CYS A 337 -78.17 -103.63 REMARK 500 ALA A 401 36.22 -82.42 REMARK 500 CYS A 441 -74.22 -111.20 REMARK 500 HIS A 461 59.53 -161.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 150 SG REMARK 620 2 CYS A 154 SG 110.8 REMARK 620 3 CYS A 212 SG 113.7 113.2 REMARK 620 4 HIS A 215 NE2 109.1 99.7 109.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 504 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 166 SG REMARK 620 2 CYS A 169 SG 110.0 REMARK 620 3 CYS A 196 SG 107.4 112.1 REMARK 620 4 CYS A 201 SG 106.0 108.1 113.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 505 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 238 SG REMARK 620 2 CYS A 241 SG 110.2 REMARK 620 3 CYS A 260 SG 114.4 117.1 REMARK 620 4 CYS A 263 SG 109.3 105.6 99.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 253 SG REMARK 620 2 HIS A 257 ND1 100.7 REMARK 620 3 CYS A 289 SG 111.7 97.1 REMARK 620 4 CYS A 293 SG 120.9 109.6 113.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 506 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 332 SG REMARK 620 2 CYS A 337 SG 119.8 REMARK 620 3 CYS A 352 SG 108.0 104.0 REMARK 620 4 CYS A 360 SG 108.0 114.2 100.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 507 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 365 SG REMARK 620 2 CYS A 368 SG 110.6 REMARK 620 3 HIS A 373 NE2 105.3 106.5 REMARK 620 4 CYS A 377 SG 105.1 121.7 106.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 508 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 418 SG REMARK 620 2 CYS A 421 SG 114.5 REMARK 620 3 CYS A 436 SG 111.8 101.3 REMARK 620 4 CYS A 441 SG 104.0 115.8 109.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 446 SG REMARK 620 2 CYS A 449 SG 115.0 REMARK 620 3 CYS A 457 SG 113.5 112.3 REMARK 620 4 HIS A 461 NE2 106.0 99.3 109.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 512 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 513 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 514 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 515 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 516 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 517 DBREF 5C9V A 137 465 UNP O60260 PRKN2_HUMAN 137 465 SEQADV 5C9V GLY A 136 UNP O60260 EXPRESSION TAG SEQADV 5C9V ALA A 319 UNP O60260 GLY 319 ENGINEERED MUTATION SEQRES 1 A 330 GLY PRO ALA GLY ARG SER ILE TYR ASN SER PHE TYR VAL SEQRES 2 A 330 TYR CYS LYS GLY PRO CYS GLN ARG VAL GLN PRO GLY LYS SEQRES 3 A 330 LEU ARG VAL GLN CYS SER THR CYS ARG GLN ALA THR LEU SEQRES 4 A 330 THR LEU THR GLN GLY PRO SER CYS TRP ASP ASP VAL LEU SEQRES 5 A 330 ILE PRO ASN ARG MET SER GLY GLU CYS GLN SER PRO HIS SEQRES 6 A 330 CYS PRO GLY THR SER ALA GLU PHE PHE PHE LYS CYS GLY SEQRES 7 A 330 ALA HIS PRO THR SER ASP LYS GLU THR SER VAL ALA LEU SEQRES 8 A 330 HIS LEU ILE ALA THR ASN SER ARG ASN ILE THR CYS ILE SEQRES 9 A 330 THR CYS THR ASP VAL ARG SER PRO VAL LEU VAL PHE GLN SEQRES 10 A 330 CYS ASN SER ARG HIS VAL ILE CYS LEU ASP CYS PHE HIS SEQRES 11 A 330 LEU TYR CYS VAL THR ARG LEU ASN ASP ARG GLN PHE VAL SEQRES 12 A 330 HIS ASP PRO GLN LEU GLY TYR SER LEU PRO CYS VAL ALA SEQRES 13 A 330 GLY CYS PRO ASN SER LEU ILE LYS GLU LEU HIS HIS PHE SEQRES 14 A 330 ARG ILE LEU GLY GLU GLU GLN TYR ASN ARG TYR GLN GLN SEQRES 15 A 330 TYR ALA ALA GLU GLU CYS VAL LEU GLN MET GLY GLY VAL SEQRES 16 A 330 LEU CYS PRO ARG PRO GLY CYS GLY ALA GLY LEU LEU PRO SEQRES 17 A 330 GLU PRO ASP GLN ARG LYS VAL THR CYS GLU GLY GLY ASN SEQRES 18 A 330 GLY LEU GLY CYS GLY PHE ALA PHE CYS ARG GLU CYS LYS SEQRES 19 A 330 GLU ALA TYR HIS GLU GLY GLU CYS SER ALA VAL PHE GLU SEQRES 20 A 330 ALA SER GLY THR THR THR GLN ALA TYR ARG VAL ASP GLU SEQRES 21 A 330 ARG ALA ALA GLU GLN ALA ARG TRP GLU ALA ALA SER LYS SEQRES 22 A 330 GLU THR ILE LYS LYS THR THR LYS PRO CYS PRO ARG CYS SEQRES 23 A 330 HIS VAL PRO VAL GLU LYS ASN GLY GLY CYS MET HIS MET SEQRES 24 A 330 LYS CYS PRO GLN PRO GLN CYS ARG LEU GLU TRP CYS TRP SEQRES 25 A 330 ASN CYS GLY CYS GLU TRP ASN ARG VAL CYS MET GLY ASP SEQRES 26 A 330 HIS TRP PHE ASP VAL HET ZN A 501 1 HET ZN A 502 1 HET ZN A 503 1 HET ZN A 504 1 HET ZN A 505 1 HET ZN A 506 1 HET ZN A 507 1 HET ZN A 508 1 HET SO4 A 509 5 HET SO4 A 510 5 HET SO4 A 511 5 HET SO4 A 512 5 HET SO4 A 513 5 HET SO4 A 514 5 HET GOL A 515 6 HET GOL A 516 6 HET GOL A 517 6 HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ZN 8(ZN 2+) FORMUL 10 SO4 6(O4 S 2-) FORMUL 16 GOL 3(C3 H8 O3) FORMUL 19 HOH *81(H2 O) HELIX 1 AA1 CYS A 182 ILE A 188 1 7 HELIX 2 AA2 LEU A 261 ASP A 274 1 14 HELIX 3 AA3 GLU A 300 LEU A 307 5 8 HELIX 4 AA4 GLY A 308 GLN A 317 1 10 HELIX 5 AA5 GLN A 317 GLN A 326 1 10 HELIX 6 AA6 SER A 378 ALA A 383 1 6 HELIX 7 AA7 ASP A 394 ALA A 401 1 8 HELIX 8 AA8 ASN A 454 TRP A 462 1 9 SHEET 1 AA1 4 ALA A 206 CYS A 212 0 SHEET 2 AA1 4 ARG A 156 CYS A 166 -1 N LYS A 161 O LYS A 211 SHEET 3 AA1 4 TYR A 147 CYS A 150 -1 N VAL A 148 O GLN A 158 SHEET 4 AA1 4 VAL A 224 ALA A 225 -1 O VAL A 224 N TYR A 149 SHEET 1 AA2 2 LEU A 174 LEU A 176 0 SHEET 2 AA2 2 GLY A 194 CYS A 196 -1 O GLU A 195 N THR A 175 SHEET 1 AA3 3 ILE A 229 ALA A 230 0 SHEET 2 AA3 3 VAL A 248 VAL A 250 -1 O VAL A 248 N ALA A 230 SHEET 3 AA3 3 VAL A 258 CYS A 260 -1 O ILE A 259 N LEU A 249 SHEET 1 AA4 2 VAL A 278 ASP A 280 0 SHEET 2 AA4 2 GLY A 284 SER A 286 -1 O SER A 286 N VAL A 278 SHEET 1 AA5 2 VAL A 330 LEU A 331 0 SHEET 2 AA5 2 GLY A 340 LEU A 341 -1 O LEU A 341 N VAL A 330 SHEET 1 AA6 2 LYS A 349 THR A 351 0 SHEET 2 AA6 2 ALA A 363 CYS A 365 -1 O PHE A 364 N VAL A 350 SHEET 1 AA7 2 THR A 415 PRO A 417 0 SHEET 2 AA7 2 PRO A 424 GLU A 426 -1 O VAL A 425 N LYS A 416 SHEET 1 AA8 2 HIS A 433 LYS A 435 0 SHEET 2 AA8 2 GLU A 444 CYS A 446 -1 O TRP A 445 N MET A 434 LINK SG CYS A 150 ZN ZN A 501 1555 1555 2.26 LINK SG CYS A 154 ZN ZN A 501 1555 1555 2.44 LINK SG CYS A 166 ZN ZN A 504 1555 1555 2.40 LINK SG CYS A 169 ZN ZN A 504 1555 1555 2.29 LINK SG CYS A 196 ZN ZN A 504 1555 1555 2.29 LINK SG CYS A 201 ZN ZN A 504 1555 1555 2.29 LINK SG CYS A 212 ZN ZN A 501 1555 1555 2.27 LINK NE2 HIS A 215 ZN ZN A 501 1555 1555 2.00 LINK SG CYS A 238 ZN ZN A 505 1555 1555 2.38 LINK SG CYS A 241 ZN ZN A 505 1555 1555 2.35 LINK SG CYS A 253 ZN ZN A 502 1555 1555 2.34 LINK ND1 HIS A 257 ZN ZN A 502 1555 1555 2.05 LINK SG CYS A 260 ZN ZN A 505 1555 1555 2.26 LINK SG CYS A 263 ZN ZN A 505 1555 1555 2.36 LINK SG CYS A 289 ZN ZN A 502 1555 1555 2.38 LINK SG CYS A 293 ZN ZN A 502 1555 1555 2.29 LINK SG CYS A 332 ZN ZN A 506 1555 1555 2.34 LINK SG CYS A 337 ZN ZN A 506 1555 1555 2.27 LINK SG CYS A 352 ZN ZN A 506 1555 1555 2.26 LINK SG CYS A 360 ZN ZN A 506 1555 1555 2.44 LINK SG CYS A 365 ZN ZN A 507 1555 1555 2.31 LINK SG CYS A 368 ZN ZN A 507 1555 1555 2.26 LINK NE2 HIS A 373 ZN ZN A 507 1555 1555 2.08 LINK SG CYS A 377 ZN ZN A 507 1555 1555 2.35 LINK SG CYS A 418 ZN ZN A 508 1555 1555 2.31 LINK SG CYS A 421 ZN ZN A 508 1555 1555 2.28 LINK SG CYS A 436 ZN ZN A 508 1555 1555 2.32 LINK SG CYS A 441 ZN ZN A 508 1555 1555 2.33 LINK SG CYS A 446 ZN ZN A 503 1555 1555 2.30 LINK SG CYS A 449 ZN ZN A 503 1555 1555 2.39 LINK SG CYS A 457 ZN ZN A 503 1555 1555 2.32 LINK NE2 HIS A 461 ZN ZN A 503 1555 1555 2.33 CISPEP 1 GLY A 152 PRO A 153 0 2.87 CISPEP 2 SER A 246 PRO A 247 0 -1.20 SITE 1 AC1 4 CYS A 150 CYS A 154 CYS A 212 HIS A 215 SITE 1 AC2 4 CYS A 253 HIS A 257 CYS A 289 CYS A 293 SITE 1 AC3 4 CYS A 446 CYS A 449 CYS A 457 HIS A 461 SITE 1 AC4 4 CYS A 166 CYS A 169 CYS A 196 CYS A 201 SITE 1 AC5 4 CYS A 238 CYS A 241 CYS A 260 CYS A 263 SITE 1 AC6 4 CYS A 332 CYS A 337 CYS A 352 CYS A 360 SITE 1 AC7 4 CYS A 365 CYS A 368 HIS A 373 CYS A 377 SITE 1 AC8 4 CYS A 418 CYS A 421 CYS A 436 CYS A 441 SITE 1 AC9 5 ARG A 163 LYS A 211 THR A 217 ARG A 420 SITE 2 AC9 5 HOH A 624 SITE 1 AD1 2 ASN A 454 ARG A 455 SITE 1 AD2 3 HIS A 279 ARG A 334 GLY A 361 SITE 1 AD3 2 ASN A 254 PRO A 294 SITE 1 AD4 5 LYS A 151 HIS A 302 ARG A 305 TYR A 312 SITE 2 AD4 5 HOH A 603 SITE 1 AD5 2 ARG A 348 TYR A 372 SITE 1 AD6 5 CYS A 368 HIS A 373 GLU A 376 CYS A 377 SITE 2 AD6 5 SER A 378 SITE 1 AD7 6 VAL A 186 LEU A 187 PRO A 189 PHE A 208 SITE 2 AD7 6 HOH A 604 HOH A 621 SITE 1 AD8 3 ASN A 295 SER A 296 LEU A 297 CRYST1 169.360 169.360 96.990 90.00 90.00 120.00 H 3 2 18 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 0.005905 0.003409 0.000000 0.00000 SCALE2 0.000000 0.006818 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010310 0.00000