HEADER LIGASE 07-MAY-13 4BM9 TITLE STRUCTURE OF THE AUTOINHIBITED PARKIN CATALYTIC DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE PARKIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UPD AND RBR DOMAIN, RESIDUES 137-465; COMPND 5 SYNONYM: PARKINSON JUVENILE DISEASE PROTEIN 2, PARKINSON DISEASE COMPND 6 PROTEIN 2, PARKIN; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA2 KEYWDS LIGASE, NEURODEGENERATIVE DISEASE EXPDTA X-RAY DIFFRACTION AUTHOR T.WAUER,D.KOMANDER REVDAT 2 14-AUG-13 4BM9 1 JRNL REVDAT 1 12-JUN-13 4BM9 0 JRNL AUTH T.WAUER,D.KOMANDER JRNL TITL STRUCTURE OF THE HUMAN PARKIN LIGASE DOMAIN IN AN JRNL TITL 2 AUTOINHIBITED STATE. JRNL REF EMBO J. V. 32 2099 2013 JRNL REFN ISSN 0261-4189 JRNL PMID 23727886 JRNL DOI 10.1038/EMBOJ.2013.125 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT 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) : 2.250 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.619 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.34 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.48 REMARK 3 NUMBER OF REFLECTIONS : 24502 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1918 REMARK 3 R VALUE (WORKING SET) : 0.1903 REMARK 3 FREE R VALUE : 0.2178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.1 REMARK 3 FREE R VALUE TEST SET COUNT : 1246 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 48.6300 - 4.6791 0.94 2568 136 0.1811 0.2080 REMARK 3 2 4.6791 - 3.7143 0.96 2577 147 0.1542 0.1749 REMARK 3 3 3.7143 - 3.2449 0.97 2560 127 0.1773 0.2063 REMARK 3 4 3.2449 - 2.9483 0.98 2600 126 0.2042 0.2338 REMARK 3 5 2.9483 - 2.7370 0.98 2605 134 0.2224 0.2569 REMARK 3 6 2.7370 - 2.5756 0.98 2586 128 0.2183 0.2778 REMARK 3 7 2.5756 - 2.4466 0.99 2598 150 0.2267 0.2348 REMARK 3 8 2.4466 - 2.3401 0.99 2571 147 0.2385 0.2556 REMARK 3 9 2.3401 - 2.2501 0.99 2591 151 0.2696 0.3016 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) : 0.21 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.60 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.006 2361 REMARK 3 ANGLE : 0.974 3212 REMARK 3 CHIRALITY : 0.066 344 REMARK 3 PLANARITY : 0.005 418 REMARK 3 DIHEDRAL : 16.629 832 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESID 142 THROUGH 227 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.6852 37.8283 40.8627 REMARK 3 T TENSOR REMARK 3 T11: 0.1429 T22: 0.1607 REMARK 3 T33: 0.3154 T12: -0.0274 REMARK 3 T13: 0.0532 T23: 0.0689 REMARK 3 L TENSOR REMARK 3 L11: 3.6699 L22: 1.8064 REMARK 3 L33: 3.5802 L12: -0.2365 REMARK 3 L13: 0.6200 L23: -1.0270 REMARK 3 S TENSOR REMARK 3 S11: -0.1087 S12: 0.0374 S13: 0.4823 REMARK 3 S21: 0.0519 S22: 0.0142 S23: 0.1748 REMARK 3 S31: -0.1695 S32: -0.0859 S33: 0.0990 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESID 228 THROUGH 327 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.5073 29.4903 32.7026 REMARK 3 T TENSOR REMARK 3 T11: 0.1446 T22: 0.2570 REMARK 3 T33: 0.1531 T12: 0.0293 REMARK 3 T13: 0.0220 T23: 0.0067 REMARK 3 L TENSOR REMARK 3 L11: 5.3074 L22: 3.2795 REMARK 3 L33: 2.7110 L12: 0.5771 REMARK 3 L13: -0.8566 L23: -0.0369 REMARK 3 S TENSOR REMARK 3 S11: 0.0540 S12: 0.6927 S13: -0.3486 REMARK 3 S21: -0.1163 S22: -0.0830 S23: 0.0320 REMARK 3 S31: 0.0795 S32: -0.0718 S33: -0.0099 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND (RESID 328 THROUGH 382 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.2630 37.5980 41.5675 REMARK 3 T TENSOR REMARK 3 T11: 0.8087 T22: 0.4265 REMARK 3 T33: 0.5610 T12: -0.1976 REMARK 3 T13: -0.1288 T23: 0.0965 REMARK 3 L TENSOR REMARK 3 L11: 1.7533 L22: 5.1590 REMARK 3 L33: 1.3574 L12: 0.8209 REMARK 3 L13: -0.6055 L23: 0.5430 REMARK 3 S TENSOR REMARK 3 S11: 0.3375 S12: -0.1642 S13: -0.1934 REMARK 3 S21: 1.2760 S22: -0.9036 S23: -1.7778 REMARK 3 S31: 0.0628 S32: 0.3815 S33: 0.1883 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND (RESID 391 THROUGH 404 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.6201 14.2401 27.2699 REMARK 3 T TENSOR REMARK 3 T11: 0.4545 T22: 0.4780 REMARK 3 T33: 0.9018 T12: -0.0458 REMARK 3 T13: -0.0453 T23: -0.2219 REMARK 3 L TENSOR REMARK 3 L11: 0.1097 L22: 5.3914 REMARK 3 L33: 6.5200 L12: 0.0739 REMARK 3 L13: 0.6231 L23: 0.1201 REMARK 3 S TENSOR REMARK 3 S11: -0.0301 S12: 0.2973 S13: -0.2044 REMARK 3 S21: -0.4234 S22: -0.0775 S23: 0.2869 REMARK 3 S31: 0.4769 S32: -0.2901 S33: 0.3001 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN A AND (RESID 414 THROUGH 465 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.2654 22.9616 36.8067 REMARK 3 T TENSOR REMARK 3 T11: 0.3042 T22: 0.2224 REMARK 3 T33: 0.2854 T12: -0.0568 REMARK 3 T13: 0.0075 T23: 0.0941 REMARK 3 L TENSOR REMARK 3 L11: 3.9238 L22: 2.8388 REMARK 3 L33: 1.4560 L12: 2.6615 REMARK 3 L13: 0.1217 L23: -0.0545 REMARK 3 S TENSOR REMARK 3 S11: -0.3499 S12: 0.5719 S13: 0.1755 REMARK 3 S21: -0.6103 S22: 0.2344 S23: 0.1779 REMARK 3 S31: 0.0441 S32: -0.0514 S33: 0.1077 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 4BM9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-MAY-13. REMARK 100 THE PDBE ID CODE IS EBI-56782. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24502 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.25 REMARK 200 RESOLUTION RANGE LOW (A) : 58.33 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 5 REMARK 200 R MERGE (I) : 0.09 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.30 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5 REMARK 200 R MERGE FOR SHELL (I) : 0.64 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.30 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.8 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M LITHIUM SULPHATE, 10 MM REMARK 280 MAGNESIUM CHLORIDE, 50 MM MES (PH 5.4) 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 84.21000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 48.61867 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 32.39367 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 84.21000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 48.61867 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 32.39367 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 84.21000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 48.61867 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 32.39367 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 84.21000 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 48.61867 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 32.39367 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 84.21000 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 48.61867 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 32.39367 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 84.21000 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 48.61867 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 32.39367 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 97.23733 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 64.78733 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 97.23733 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 64.78733 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 97.23733 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 64.78733 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 97.23733 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 64.78733 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 97.23733 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 64.78733 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 97.23733 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 64.78733 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 18930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 83320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -586.4 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 350 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 97.18100 REMARK 350 BIOMT1 4 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 4 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 97.18100 REMARK 350 BIOMT1 5 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 5 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 6 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 97.18100 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 A1475 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2039 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2082 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 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 357 REMARK 465 LEU A 358 REMARK 465 GLY A 359 REMARK 465 CYS A 360 REMARK 465 GLY A 361 REMARK 465 SER A 384 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 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 GLN A 155 CG CD OE1 NE2 REMARK 470 GLU A 195 CG CD OE1 OE2 REMARK 470 GLN A 197 CG CD OE1 NE2 REMARK 470 ARG A 256 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 ASN A 295 CG OD1 ND2 REMARK 470 GLU A 310 CB CG CD OE1 OE2 REMARK 470 ASN A 313 CG OD1 ND2 REMARK 470 ARG A 334 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 344 CG CD OE1 OE2 REMARK 470 ASP A 346 CG OD1 OD2 REMARK 470 GLU A 353 CG CD OE1 OE2 REMARK 470 GLU A 370 CG CD OE1 OE2 REMARK 470 GLU A 374 CG CD OE1 OE2 REMARK 470 TYR A 391 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 392 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 395 CG CD OE1 OE2 REMARK 470 ARG A 396 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 399 CG CD OE1 OE2 REMARK 470 ARG A 402 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 413 CG CD CE NZ REMARK 470 GLU A 426 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 OH TYR A 143 OD2 ASP A 464 2.08 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 PRO A 199 -73.47 -34.78 REMARK 500 THR A 242 -1.50 61.25 REMARK 500 CYS A 441 -71.84 -110.79 REMARK 500 HIS A 461 55.87 -153.39 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 A1466 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 150 SG REMARK 620 2 CYS A 154 SG 114.1 REMARK 620 3 CYS A 212 SG 113.3 112.4 REMARK 620 4 HIS A 215 NE2 108.0 99.2 108.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1467 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 253 SG REMARK 620 2 HIS A 257 ND1 93.0 REMARK 620 3 CYS A 293 SG 116.4 114.8 REMARK 620 4 CYS A 289 SG 113.6 97.9 117.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1468 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 446 SG REMARK 620 2 CYS A 449 SG 112.9 REMARK 620 3 CYS A 457 SG 113.1 115.1 REMARK 620 4 HIS A 461 NE2 103.2 103.9 107.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1469 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 196 SG REMARK 620 2 CYS A 201 SG 115.0 REMARK 620 3 CYS A 166 SG 110.7 107.9 REMARK 620 4 CYS A 169 SG 107.6 110.1 105.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1470 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 238 SG REMARK 620 2 CYS A 241 SG 105.7 REMARK 620 3 CYS A 260 SG 115.6 115.0 REMARK 620 4 CYS A 263 SG 108.3 109.8 102.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1471 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 332 SG REMARK 620 2 CYS A 337 SG 107.8 REMARK 620 3 CYS A 352 SG 91.9 102.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1472 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 377 SG REMARK 620 2 HIS A 373 NE2 99.7 REMARK 620 3 CYS A 365 SG 111.7 98.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1473 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 418 SG REMARK 620 2 CYS A 421 SG 110.7 REMARK 620 3 CYS A 436 SG 114.7 101.5 REMARK 620 4 CYS A 441 SG 104.9 116.5 109.0 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 A1466 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1467 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1468 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1469 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1470 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1471 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1472 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1473 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1474 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1475 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1476 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1477 DBREF 4BM9 A 137 465 UNP O60260 PRKN2_HUMAN 137 465 SEQRES 1 A 329 PRO ALA GLY ARG SER ILE TYR ASN SER PHE TYR VAL TYR SEQRES 2 A 329 CYS LYS GLY PRO CYS GLN ARG VAL GLN PRO GLY LYS LEU SEQRES 3 A 329 ARG VAL GLN CYS SER THR CYS ARG GLN ALA THR LEU THR SEQRES 4 A 329 LEU THR GLN GLY PRO SER CYS TRP ASP ASP VAL LEU ILE SEQRES 5 A 329 PRO ASN ARG MET SER GLY GLU CYS GLN SER PRO HIS CYS SEQRES 6 A 329 PRO GLY THR SER ALA GLU PHE PHE PHE LYS CYS GLY ALA SEQRES 7 A 329 HIS PRO THR SER ASP LYS GLU THR SER VAL ALA LEU HIS SEQRES 8 A 329 LEU ILE ALA THR ASN SER ARG ASN ILE THR CYS ILE THR SEQRES 9 A 329 CYS THR ASP VAL ARG SER PRO VAL LEU VAL PHE GLN CYS SEQRES 10 A 329 ASN SER ARG HIS VAL ILE CYS LEU ASP CYS PHE HIS LEU SEQRES 11 A 329 TYR CYS VAL THR ARG LEU ASN ASP ARG GLN PHE VAL HIS SEQRES 12 A 329 ASP PRO GLN LEU GLY TYR SER LEU PRO CYS VAL ALA GLY SEQRES 13 A 329 CYS PRO ASN SER LEU ILE LYS GLU LEU HIS HIS PHE ARG SEQRES 14 A 329 ILE LEU GLY GLU GLU GLN TYR ASN ARG TYR GLN GLN TYR SEQRES 15 A 329 GLY ALA GLU GLU CYS VAL LEU GLN MET GLY GLY VAL LEU SEQRES 16 A 329 CYS PRO ARG PRO GLY CYS GLY ALA GLY LEU LEU PRO GLU SEQRES 17 A 329 PRO ASP GLN ARG LYS VAL THR CYS GLU GLY GLY ASN GLY SEQRES 18 A 329 LEU GLY CYS GLY PHE ALA PHE CYS ARG GLU CYS LYS GLU SEQRES 19 A 329 ALA TYR HIS GLU GLY GLU CYS SER ALA VAL PHE GLU ALA SEQRES 20 A 329 SER GLY THR THR THR GLN ALA TYR ARG VAL ASP GLU ARG SEQRES 21 A 329 ALA ALA GLU GLN ALA ARG TRP GLU ALA ALA SER LYS GLU SEQRES 22 A 329 THR ILE LYS LYS THR THR LYS PRO CYS PRO ARG CYS HIS SEQRES 23 A 329 VAL PRO VAL GLU LYS ASN GLY GLY CYS MET HIS MET LYS SEQRES 24 A 329 CYS PRO GLN PRO GLN CYS ARG LEU GLU TRP CYS TRP ASN SEQRES 25 A 329 CYS GLY CYS GLU TRP ASN ARG VAL CYS MET GLY ASP HIS SEQRES 26 A 329 TRP PHE ASP VAL HET ZN A1466 1 HET ZN A1467 1 HET ZN A1468 1 HET ZN A1469 1 HET ZN A1470 1 HET ZN A1471 1 HET ZN A1472 1 HET ZN A1473 1 HET SO4 A1474 5 HET SO4 A1475 5 HET SO4 A1476 5 HET GOL A1477 6 HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETNAM ZN ZINC ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 SO4 3(O4 S 2-) FORMUL 3 GOL C3 H8 O3 FORMUL 4 ZN 8(ZN 2+) FORMUL 5 HOH *87(H2 O) HELIX 1 1 CYS A 182 ILE A 188 1 7 HELIX 2 2 LEU A 261 ASP A 274 1 14 HELIX 3 3 GLU A 300 LEU A 307 5 8 HELIX 4 4 GLY A 308 GLN A 317 1 10 HELIX 5 5 GLN A 317 MET A 327 1 11 HELIX 6 6 SER A 378 GLU A 382 5 5 HELIX 7 7 ASP A 394 ALA A 401 1 8 HELIX 8 8 ASN A 454 TRP A 462 1 9 SHEET 1 AA 4 ALA A 206 CYS A 212 0 SHEET 2 AA 4 ARG A 156 CYS A 166 -1 O LYS A 161 N LYS A 211 SHEET 3 AA 4 TYR A 147 CYS A 150 -1 O VAL A 148 N GLN A 158 SHEET 4 AA 4 VAL A 224 ALA A 225 -1 O VAL A 224 N TYR A 149 SHEET 1 AB 2 LEU A 174 LEU A 176 0 SHEET 2 AB 2 GLY A 194 CYS A 196 -1 O GLU A 195 N THR A 175 SHEET 1 AC 3 ILE A 229 ALA A 230 0 SHEET 2 AC 3 VAL A 248 VAL A 250 -1 O VAL A 248 N ALA A 230 SHEET 3 AC 3 VAL A 258 CYS A 260 -1 O ILE A 259 N LEU A 249 SHEET 1 AD 2 VAL A 278 ASP A 280 0 SHEET 2 AD 2 GLY A 284 SER A 286 -1 O GLY A 284 N ASP A 280 SHEET 1 AE 2 VAL A 330 LEU A 331 0 SHEET 2 AE 2 GLY A 340 LEU A 341 -1 O LEU A 341 N VAL A 330 SHEET 1 AF 2 LYS A 349 THR A 351 0 SHEET 2 AF 2 ALA A 363 CYS A 365 -1 O PHE A 364 N VAL A 350 SHEET 1 AG 2 THR A 415 PRO A 417 0 SHEET 2 AG 2 PRO A 424 GLU A 426 -1 O VAL A 425 N LYS A 416 SHEET 1 AH 2 HIS A 433 LYS A 435 0 SHEET 2 AH 2 GLU A 444 CYS A 446 -1 O TRP A 445 N MET A 434 LINK ZN ZN A1466 SG CYS A 150 1555 1555 2.30 LINK ZN ZN A1466 SG CYS A 154 1555 1555 2.39 LINK ZN ZN A1466 SG CYS A 212 1555 1555 2.34 LINK ZN ZN A1466 NE2 HIS A 215 1555 1555 2.05 LINK ZN ZN A1467 SG CYS A 253 1555 1555 2.35 LINK ZN ZN A1467 ND1 HIS A 257 1555 1555 1.83 LINK ZN ZN A1467 SG CYS A 293 1555 1555 2.46 LINK ZN ZN A1467 SG CYS A 289 1555 1555 2.44 LINK ZN ZN A1468 SG CYS A 446 1555 1555 2.26 LINK ZN ZN A1468 SG CYS A 449 1555 1555 2.36 LINK ZN ZN A1468 SG CYS A 457 1555 1555 2.24 LINK ZN ZN A1468 NE2 HIS A 461 1555 1555 2.09 LINK ZN ZN A1469 SG CYS A 196 1555 1555 2.26 LINK ZN ZN A1469 SG CYS A 201 1555 1555 2.29 LINK ZN ZN A1469 SG CYS A 166 1555 1555 2.42 LINK ZN ZN A1469 SG CYS A 169 1555 1555 2.21 LINK ZN ZN A1470 SG CYS A 241 1555 1555 2.35 LINK ZN ZN A1470 SG CYS A 260 1555 1555 2.32 LINK ZN ZN A1470 SG CYS A 263 1555 1555 2.33 LINK ZN ZN A1470 SG CYS A 238 1555 1555 2.34 LINK ZN ZN A1471 SG CYS A 337 1555 1555 2.15 LINK ZN ZN A1471 SG CYS A 352 1555 1555 2.11 LINK ZN ZN A1471 SG CYS A 332 1555 1555 2.56 LINK ZN ZN A1472 NE2 HIS A 373 1555 1555 1.93 LINK ZN ZN A1472 SG CYS A 365 1555 1555 2.39 LINK ZN ZN A1472 SG CYS A 377 1555 1555 2.30 LINK ZN ZN A1473 SG CYS A 421 1555 1555 2.31 LINK ZN ZN A1473 SG CYS A 436 1555 1555 2.33 LINK ZN ZN A1473 SG CYS A 441 1555 1555 2.28 LINK ZN ZN A1473 SG CYS A 418 1555 1555 2.32 CISPEP 1 GLY A 152 PRO A 153 0 1.67 CISPEP 2 SER A 246 PRO A 247 0 -1.11 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 3 CYS A 332 CYS A 337 CYS A 352 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 4 ARG A 163 LYS A 211 ARG A 420 HOH A2045 SITE 1 BC1 2 ASN A 454 ARG A 455 SITE 1 BC2 5 LYS A 151 HIS A 302 ARG A 305 TYR A 312 SITE 2 BC2 5 HOH A2087 SITE 1 BC3 3 LYS A 416 TRP A 447 ASN A 448 CRYST1 168.420 168.420 97.181 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 0.005938 0.003428 0.000000 0.00000 SCALE2 0.000000 0.006856 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010290 0.00000