HEADER LIGASE 01-MAR-23 8IKT TITLE TERNARY TRANS-COMPLEX OF PHOSPHO-PARKIN WITH CIS ACT AND PUB COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE PARKIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PARKIN,PARKIN RBR E3 UBIQUITIN-PROTEIN LIGASE,PARKINSON COMPND 5 JUVENILE DISEASE PROTEIN 2,PARKINSON DISEASE PROTEIN 2; COMPND 6 EC: 2.3.2.31; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 OTHER_DETAILS: LTRVDL CORRESPONDS TO THE 102 TO 107 REGION OF THE COMPND 10 PROTEIN. THE MISMATCH IN THE ALIGNMENT IS DUE TO THE MISSING ELECTRON COMPND 11 DENSITY OF THE REGION IN BETWEEN.; COMPND 12 MOL_ID: 2; COMPND 13 MOLECULE: UBIQUITIN; COMPND 14 CHAIN: B; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 3; COMPND 17 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE PARKIN; COMPND 18 CHAIN: C; COMPND 19 SYNONYM: PARKIN,PARKIN RBR E3 UBIQUITIN-PROTEIN LIGASE,PARKINSON COMPND 20 JUVENILE DISEASE PROTEIN 2,PARKINSON DISEASE PROTEIN 2; COMPND 21 EC: 2.3.2.31; COMPND 22 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: PRKN, PARK2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: UBA52, UBCEP2; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_COMMON: HUMAN; SOURCE 18 ORGANISM_TAXID: 9606; SOURCE 19 GENE: PRKN, PARK2; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 21 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS E3 LIGASE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR D.R.LENKA,A.KUMAR REVDAT 1 11-SEP-24 8IKT 0 JRNL AUTH D.LENKA,S.DAHE,O.ANTICO,P.SAHOO,A.R.PRESCOTT,M.M.K.MUQIT, JRNL AUTH 2 A.KUMAR JRNL TITL ADDITIONAL FEEDFORWARD MECHANISM OF PARKIN ACTIVATION VIA JRNL TITL 2 BINDING OF PHOSPHO-UBL AND RING0 IN TRANS JRNL REF ELIFE 2024 JRNL REFN ESSN 2050-084X JRNL DOI 10.7554/ELIFE.96699.2 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.42 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 12333 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.306 REMARK 3 FREE R VALUE TEST SET COUNT : 691 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 888 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3020 REMARK 3 BIN FREE R VALUE SET COUNT : 55 REMARK 3 BIN FREE R VALUE : 0.3070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2977 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 52 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.81400 REMARK 3 B22 (A**2) : -1.81400 REMARK 3 B33 (A**2) : 5.88300 REMARK 3 B12 (A**2) : -0.90700 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.313 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.288 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 32.393 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3117 ; 0.005 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4223 ; 0.844 ; 1.656 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 395 ; 5.887 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 155 ;33.857 ;22.581 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 508 ;14.863 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ; 9.993 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 411 ; 0.063 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2335 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1531 ; 0.198 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2127 ; 0.303 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 167 ; 0.121 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1552 ; 1.836 ; 6.443 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1935 ; 2.945 ; 9.647 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1563 ; 1.841 ; 6.479 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2279 ; 2.729 ; 9.654 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 3115 ; 0.237 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 8IKT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1300035905. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-FEB-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM07 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13050 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 38.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : 0.14400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.72 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 8IKM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.3 M SODIUM NITRATE, 0.3 SODIUM REMARK 280 PHOSPHATE DIBASIC, 0.3 M AMMONIUM SULFATE, IMIDAZOLE, MES REMARK 280 MONOHYDRATE (ACID), 25% V/V MPD, 25% PEG 1000, 25% W/V PEG 3350, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-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 68.99600 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 34.49800 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 34.49800 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 68.99600 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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. (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 SER A 76 REMARK 465 GLY A 77 REMARK 465 GLN A 78 REMARK 465 GLU A 79 REMARK 465 MET A 80 REMARK 465 ASN A 81 REMARK 465 ALA A 82 REMARK 465 THR A 83 REMARK 465 GLY A 84 REMARK 465 GLY A 85 REMARK 465 ASP A 86 REMARK 465 ASP A 87 REMARK 465 PRO A 88 REMARK 465 ARG A 89 REMARK 465 ASN A 90 REMARK 465 ALA A 91 REMARK 465 ALA A 92 REMARK 465 GLY A 93 REMARK 465 GLY A 94 REMARK 465 CYS A 95 REMARK 465 GLU A 96 REMARK 465 ARG A 97 REMARK 465 GLU A 98 REMARK 465 PRO A 99 REMARK 465 GLN A 100 REMARK 465 SER A 101 REMARK 465 SER A 108 REMARK 465 SER A 109 REMARK 465 SER A 110 REMARK 465 VAL A 111 REMARK 465 LEU A 112 REMARK 465 PRO A 113 REMARK 465 GLY A 114 REMARK 465 ASP A 115 REMARK 465 SER A 116 REMARK 465 VAL A 117 REMARK 465 GLY A 118 REMARK 465 LEU A 119 REMARK 465 ALA A 120 REMARK 465 VAL A 121 REMARK 465 ILE A 122 REMARK 465 LEU A 123 REMARK 465 HIS A 124 REMARK 465 THR A 125 REMARK 465 ASP A 126 REMARK 465 SER A 127 REMARK 465 ARG A 128 REMARK 465 LYS A 129 REMARK 465 ASP A 130 REMARK 465 SER A 131 REMARK 465 PRO A 132 REMARK 465 PRO A 133 REMARK 465 ALA A 134 REMARK 465 GLY A 135 REMARK 465 SER 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 ILE A 142 REMARK 465 TYR A 143 REMARK 465 GLY A 354 REMARK 465 GLY A 355 REMARK 465 ALA A 379 REMARK 465 VAL A 380 REMARK 465 PHE A 381 REMARK 465 GLU A 382 REMARK 465 ASN A 383 REMARK 465 LEU A 384 REMARK 465 TYR A 385 REMARK 465 PHE A 386 REMARK 465 GLN A 387 REMARK 465 PRO C 73 REMARK 465 TRP C 74 REMARK 465 ARG C 75 REMARK 465 LYS C 76 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 178 CG CD OE1 NE2 REMARK 470 HIS A 200 CG ND1 CD2 CE1 NE2 REMARK 470 GLN A 282 CG CD OE1 NE2 REMARK 470 GLU A 310 CG CD OE1 OE2 REMARK 470 ARG A 334 CZ NH1 NH2 REMARK 470 GLU A 353 CG CD OE1 OE2 REMARK 470 ASN A 356 CG OD1 ND2 REMARK 470 GLU B 24 CG CD OE1 OE2 REMARK 470 ARG B 54 CZ NH1 NH2 REMARK 470 LYS B 63 CD CE NZ REMARK 470 GLN C 40 CD OE1 NE2 REMARK 470 ARG C 42 CZ NH1 NH2 REMARK 470 LYS C 48 CD CE NZ REMARK 470 ARG C 51 CD NE CZ NH1 NH2 REMARK 470 ARG C 72 CG CD NE CZ NH1 NH2 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 O GLY B 75 ND 3CN B 101 2.03 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 SER A 218 -178.28 -64.51 REMARK 500 LEU A 226 77.53 -102.45 REMARK 500 PRO A 247 -168.22 -78.90 REMARK 500 GLN A 252 33.23 -90.26 REMARK 500 CYS A 337 -104.52 -116.61 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 506 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 150 SG REMARK 620 2 CYS A 154 SG 111.9 REMARK 620 3 CYS A 212 SG 97.7 113.2 REMARK 620 4 HIS A 215 NE2 119.8 99.9 115.1 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 166 SG REMARK 620 2 CYS A 169 SG 116.3 REMARK 620 3 CYS A 196 SG 95.7 118.9 REMARK 620 4 CYS A 201 SG 102.5 118.4 101.4 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 238 SG REMARK 620 2 CYS A 241 SG 101.0 REMARK 620 3 CYS A 260 SG 108.3 129.9 REMARK 620 4 CYS A 263 SG 107.0 104.6 104.6 REMARK 620 N 1 2 3 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 253 SG REMARK 620 2 HIS A 257 ND1 121.7 REMARK 620 3 CYS A 289 SG 106.5 101.0 REMARK 620 4 CYS A 293 SG 116.9 103.2 105.5 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 332 SG REMARK 620 2 CYS A 337 SG 107.4 REMARK 620 3 CYS A 352 SG 91.9 109.5 REMARK 620 4 CYS A 360 SG 115.0 113.4 117.5 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 365 SG REMARK 620 2 CYS A 368 SG 105.5 REMARK 620 3 HIS A 373 NE2 104.9 102.9 REMARK 620 4 CYS A 377 SG 119.5 114.6 107.8 REMARK 620 N 1 2 3 DBREF 8IKT A 77 382 UNP O60260 PRKN_HUMAN 77 382 DBREF 8IKT B 1 75 UNP P62987 RL40_HUMAN 1 75 DBREF 8IKT C 1 76 UNP O60260 PRKN_HUMAN 1 76 SEQADV 8IKT SER A 76 UNP O60260 EXPRESSION TAG SEQADV 8IKT CYS A 347 UNP O60260 GLN 347 ENGINEERED MUTATION SEQADV 8IKT ASN A 383 UNP O60260 EXPRESSION TAG SEQADV 8IKT LEU A 384 UNP O60260 EXPRESSION TAG SEQADV 8IKT TYR A 385 UNP O60260 EXPRESSION TAG SEQADV 8IKT PHE A 386 UNP O60260 EXPRESSION TAG SEQADV 8IKT GLN A 387 UNP O60260 EXPRESSION TAG SEQRES 1 A 312 SER GLY GLN GLU MET ASN ALA THR GLY GLY ASP ASP PRO SEQRES 2 A 312 ARG ASN ALA ALA GLY GLY CYS GLU ARG GLU PRO GLN SER SEQRES 3 A 312 LEU THR ARG VAL ASP LEU SER SER SER VAL LEU PRO GLY SEQRES 4 A 312 ASP SER VAL GLY LEU ALA VAL ILE LEU HIS THR ASP SER SEQRES 5 A 312 ARG LYS ASP SER PRO PRO ALA GLY SER PRO ALA GLY ARG SEQRES 6 A 312 SER ILE TYR ASN SER PHE TYR VAL TYR CYS LYS GLY PRO SEQRES 7 A 312 CYS GLN ARG VAL GLN PRO GLY LYS LEU ARG VAL GLN CYS SEQRES 8 A 312 SER THR CYS ARG GLN ALA THR LEU THR LEU THR GLN GLY SEQRES 9 A 312 PRO SER CYS TRP ASP ASP VAL LEU ILE PRO ASN ARG MET SEQRES 10 A 312 SER GLY GLU CYS GLN SER PRO HIS CYS PRO GLY THR SER SEQRES 11 A 312 ALA GLU PHE PHE PHE LYS CYS GLY ALA HIS PRO THR SER SEQRES 12 A 312 ASP LYS GLU THR SER VAL ALA LEU HIS LEU ILE ALA THR SEQRES 13 A 312 ASN SER ARG ASN ILE THR CYS ILE THR CYS THR ASP VAL SEQRES 14 A 312 ARG SER PRO VAL LEU VAL PHE GLN CYS ASN SER ARG HIS SEQRES 15 A 312 VAL ILE CYS LEU ASP CYS PHE HIS LEU TYR CYS VAL THR SEQRES 16 A 312 ARG LEU ASN ASP ARG GLN PHE VAL HIS ASP PRO GLN LEU SEQRES 17 A 312 GLY TYR SER LEU PRO CYS VAL ALA GLY CYS PRO ASN SER SEQRES 18 A 312 LEU ILE LYS GLU LEU HIS HIS PHE ARG ILE LEU GLY GLU SEQRES 19 A 312 GLU GLN TYR ASN ARG TYR GLN GLN TYR GLY ALA GLU GLU SEQRES 20 A 312 CYS VAL LEU GLN MET GLY GLY VAL LEU CYS PRO ARG PRO SEQRES 21 A 312 GLY CYS GLY ALA GLY LEU LEU PRO GLU PRO ASP CYS ARG SEQRES 22 A 312 LYS VAL THR CYS GLU GLY GLY ASN GLY LEU GLY CYS GLY SEQRES 23 A 312 PHE ALA PHE CYS ARG GLU CYS LYS GLU ALA TYR HIS GLU SEQRES 24 A 312 GLY GLU CYS SER ALA VAL PHE GLU ASN LEU TYR PHE GLN SEQRES 1 B 75 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 75 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 75 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 75 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 75 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SEP SEQRES 6 B 75 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY SEQRES 1 C 76 MET ILE VAL PHE VAL ARG PHE ASN SER SER HIS GLY PHE SEQRES 2 C 76 PRO VAL GLU VAL ASP SER ASP THR SER ILE PHE GLN LEU SEQRES 3 C 76 LYS GLU VAL VAL ALA LYS ARG GLN GLY VAL PRO ALA ASP SEQRES 4 C 76 GLN LEU ARG VAL ILE PHE ALA GLY LYS GLU LEU ARG ASN SEQRES 5 C 76 ASP TRP THR VAL GLN ASN CYS ASP LEU ASP GLN GLN SEP SEQRES 6 C 76 ILE VAL HIS ILE VAL GLN ARG PRO TRP ARG LYS MODRES 8IKT SEP B 65 SER MODIFIED RESIDUE MODRES 8IKT SEP C 65 SER MODIFIED RESIDUE HET SEP B 65 10 HET SEP C 65 10 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 GOL A 507 6 HET MPD A 508 8 HET 3CN B 101 4 HET GOL C 101 6 HETNAM SEP PHOSPHOSERINE HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM 3CN 3-AMINOPROPANE HETSYN SEP PHOSPHONOSERINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 SEP 2(C3 H8 N O6 P) FORMUL 4 ZN 6(ZN 2+) FORMUL 10 GOL 2(C3 H8 O3) FORMUL 11 MPD C6 H14 O2 FORMUL 12 3CN C3 H9 N FORMUL 14 HOH *52(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 MET A 327 1 20 HELIX 5 AA5 THR B 22 GLY B 35 1 14 HELIX 6 AA6 LEU B 56 ASN B 60 5 5 HELIX 7 AA7 SER C 22 GLY C 35 1 14 HELIX 8 AA8 PRO C 37 ASP C 39 5 3 SHEET 1 AA1 6 ALA A 206 CYS A 212 0 SHEET 2 AA1 6 ARG A 156 CYS A 166 -1 N ARG A 163 O PHE A 209 SHEET 3 AA1 6 PHE A 146 CYS A 150 -1 N PHE A 146 O GLY A 160 SHEET 4 AA1 6 VAL A 224 ALA A 230 -1 O LEU A 226 N TYR A 147 SHEET 5 AA1 6 VAL A 248 VAL A 250 -1 O VAL A 250 N LEU A 228 SHEET 6 AA1 6 VAL A 258 CYS A 260 -1 O ILE A 259 N LEU A 249 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 2 VAL A 278 ASP A 280 0 SHEET 2 AA3 2 GLY A 284 SER A 286 -1 O GLY A 284 N ASP A 280 SHEET 1 AA4 5 VAL A 330 LEU A 331 0 SHEET 2 AA4 5 GLY A 340 LEU A 342 -1 O LEU A 341 N VAL A 330 SHEET 3 AA4 5 THR B 66 ARG B 72 1 O LEU B 71 N LEU A 342 SHEET 4 AA4 5 GLN B 2 THR B 7 1 N PHE B 4 O LEU B 67 SHEET 5 AA4 5 THR B 12 GLU B 16 -1 O ILE B 13 N VAL B 5 SHEET 1 AA5 5 VAL A 330 LEU A 331 0 SHEET 2 AA5 5 GLY A 340 LEU A 342 -1 O LEU A 341 N VAL A 330 SHEET 3 AA5 5 THR B 66 ARG B 72 1 O LEU B 71 N LEU A 342 SHEET 4 AA5 5 GLN B 41 PHE B 45 -1 N ILE B 44 O HIS B 68 SHEET 5 AA5 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 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 5 PHE C 13 GLU C 16 0 SHEET 2 AA7 5 ILE C 2 PHE C 7 -1 N VAL C 3 O VAL C 15 SHEET 3 AA7 5 ILE C 66 GLN C 71 1 O VAL C 67 N PHE C 4 SHEET 4 AA7 5 LEU C 41 PHE C 45 -1 N ILE C 44 O HIS C 68 SHEET 5 AA7 5 LYS C 48 LEU C 50 -1 O LEU C 50 N VAL C 43 LINK SG CYS A 347 CA 3CN B 101 1555 1555 1.66 LINK C GLU B 64 N SEP B 65 1555 1555 1.34 LINK C SEP B 65 N THR B 66 1555 1555 1.34 LINK C GLY B 75 ND 3CN B 101 1555 1555 1.35 LINK C GLN C 64 N SEP C 65 1555 1555 1.34 LINK C SEP C 65 N ILE C 66 1555 1555 1.34 LINK SG CYS A 150 ZN ZN A 506 1555 1555 2.32 LINK SG CYS A 154 ZN ZN A 506 1555 1555 2.33 LINK SG CYS A 166 ZN ZN A 503 1555 1555 2.34 LINK SG CYS A 169 ZN ZN A 503 1555 1555 2.33 LINK SG CYS A 196 ZN ZN A 503 1555 1555 2.33 LINK SG CYS A 201 ZN ZN A 503 1555 1555 2.33 LINK SG CYS A 212 ZN ZN A 506 1555 1555 2.33 LINK NE2 HIS A 215 ZN ZN A 506 1555 1555 1.83 LINK SG CYS A 238 ZN ZN A 504 1555 1555 2.34 LINK SG CYS A 241 ZN ZN A 504 1555 1555 2.33 LINK SG CYS A 253 ZN ZN A 501 1555 1555 2.34 LINK ND1 HIS A 257 ZN ZN A 501 1555 1555 1.94 LINK SG CYS A 260 ZN ZN A 504 1555 1555 2.33 LINK SG CYS A 263 ZN ZN A 504 1555 1555 2.33 LINK SG CYS A 289 ZN ZN A 501 1555 1555 2.33 LINK SG CYS A 293 ZN ZN A 501 1555 1555 2.34 LINK SG CYS A 332 ZN ZN A 505 1555 1555 2.33 LINK SG CYS A 337 ZN ZN A 505 1555 1555 2.33 LINK SG CYS A 352 ZN ZN A 505 1555 1555 2.33 LINK SG CYS A 360 ZN ZN A 505 1555 1555 2.33 LINK SG CYS A 365 ZN ZN A 502 1555 1555 2.34 LINK SG CYS A 368 ZN ZN A 502 1555 1555 2.34 LINK NE2 HIS A 373 ZN ZN A 502 1555 1555 2.02 LINK SG CYS A 377 ZN ZN A 502 1555 1555 2.34 CISPEP 1 GLY A 152 PRO A 153 0 3.48 CISPEP 2 SER A 246 PRO A 247 0 -5.98 CRYST1 82.764 82.764 103.494 90.00 90.00 120.00 P 32 2 1 6 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 0.012083 0.006976 0.000000 0.00000 SCALE2 0.000000 0.013952 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009662 0.00000