HEADER HYDROLASE 11-APR-19 6OJE TITLE DIMERIC STRUCTURE OF LRRK2 GTPASE DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEUCINE-RICH REPEAT SERINE/THREONINE-PROTEIN KINASE 2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: GTPASE DOMAIN OF LEUCINE-RICH REPEAT KINASE 2; COMPND 5 SYNONYM: DARDARIN, LRRK2; COMPND 6 EC: 2.7.11.1; COMPND 7 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: LRRK2, PARK8; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETDUET1 KEYWDS PARKINSON'S DISEASE, LRRK2, GTPASE, DIMER, INTERSWITCH, COMPLEX, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Q.Q.HOANG,C.X.WU,J.LIAO,Y.PARK REVDAT 2 11-OCT-23 6OJE 1 REMARK REVDAT 1 14-OCT-20 6OJE 0 JRNL AUTH C.X.WU,J.LIAO,Y.PARK,N.C.HOANG,V.A.ENGEL,R.SANISHVILI, JRNL AUTH 2 Y.TAKAGI,S.M.JOHNSON,M.WANG,M.FEDERICI,R.J.NICHOLS, JRNL AUTH 3 M.R.COOKSON,Q.Q.HOANG JRNL TITL STRUCTURAL BASIS FOR CONFORMATIONAL PLASTICITY IN THE GTPASE JRNL TITL 2 DOMAIN OF THE PARKINSON'S DISEASE-ASSOCIATED PROTEIN LRRK2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0253 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 27245 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1458 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1924 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.51 REMARK 3 BIN R VALUE (WORKING SET) : 0.0690 REMARK 3 BIN FREE R VALUE SET COUNT : 125 REMARK 3 BIN FREE R VALUE : 0.0790 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2893 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 60 REMARK 3 SOLVENT ATOMS : 240 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.28000 REMARK 3 B22 (A**2) : -13.90000 REMARK 3 B33 (A**2) : 5.62000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 7.23000 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): 0.029 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.049 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.426 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3097 ; 0.004 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2894 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4202 ; 1.366 ; 1.670 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6695 ; 1.200 ; 1.596 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 389 ; 6.921 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 148 ;28.555 ;21.892 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 556 ;16.806 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;12.935 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 416 ; 0.052 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3436 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 654 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 5991 ; 1.127 ; 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1333 A 1518 REMARK 3 ORIGIN FOR THE GROUP (A): -11.1665 -2.8584 62.5240 REMARK 3 T TENSOR REMARK 3 T11: 0.0329 T22: 0.0034 REMARK 3 T33: 0.0104 T12: -0.0020 REMARK 3 T13: -0.0011 T23: -0.0005 REMARK 3 L TENSOR REMARK 3 L11: 0.0643 L22: 0.0318 REMARK 3 L33: 0.2753 L12: 0.0296 REMARK 3 L13: -0.0170 L23: -0.0775 REMARK 3 S TENSOR REMARK 3 S11: 0.0125 S12: 0.0131 S13: -0.0035 REMARK 3 S21: -0.0067 S22: 0.0072 S23: 0.0025 REMARK 3 S31: 0.0478 S32: -0.0085 S33: -0.0197 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1333 B 1519 REMARK 3 ORIGIN FOR THE GROUP (A): 5.8437 11.7132 48.4261 REMARK 3 T TENSOR REMARK 3 T11: 0.0197 T22: 0.0092 REMARK 3 T33: 0.0137 T12: 0.0012 REMARK 3 T13: 0.0008 T23: 0.0003 REMARK 3 L TENSOR REMARK 3 L11: 0.1152 L22: 0.0678 REMARK 3 L33: 0.1345 L12: 0.0746 REMARK 3 L13: 0.0126 L23: -0.0395 REMARK 3 S TENSOR REMARK 3 S11: -0.0196 S12: 0.0065 S13: -0.0227 REMARK 3 S21: -0.0011 S22: 0.0100 S23: -0.0218 REMARK 3 S31: -0.0184 S32: -0.0245 S33: 0.0097 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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 THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 6OJE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-APR-19. REMARK 100 THE DEPOSITION ID IS D_1000240737. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0331 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31247 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.45700 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: ROCCOR DOMAIN (3DPU) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM KSCN, 25% PEGMME 2000, 0.1M REMARK 280 BISTRIS PH 6.5, MICROBATCH, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 51.84400 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -96.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 MET A 1315 REMARK 465 GLY A 1316 REMARK 465 SER A 1317 REMARK 465 SER A 1318 REMARK 465 HIS A 1319 REMARK 465 HIS A 1320 REMARK 465 HIS A 1321 REMARK 465 HIS A 1322 REMARK 465 HIS A 1323 REMARK 465 HIS A 1324 REMARK 465 SER A 1325 REMARK 465 GLN A 1326 REMARK 465 ASP A 1327 REMARK 465 PRO A 1328 REMARK 465 ALA A 1329 REMARK 465 VAL A 1330 REMARK 465 PRO A 1331 REMARK 465 TYR A 1332 REMARK 465 VAL A 1519 REMARK 465 GLY A 1520 REMARK 465 MET B 1315 REMARK 465 GLY B 1316 REMARK 465 SER B 1317 REMARK 465 SER B 1318 REMARK 465 HIS B 1319 REMARK 465 HIS B 1320 REMARK 465 HIS B 1321 REMARK 465 HIS B 1322 REMARK 465 HIS B 1323 REMARK 465 HIS B 1324 REMARK 465 SER B 1325 REMARK 465 GLN B 1326 REMARK 465 ASP B 1327 REMARK 465 PRO B 1328 REMARK 465 ALA B 1329 REMARK 465 VAL B 1330 REMARK 465 PRO B 1331 REMARK 465 TYR B 1332 REMARK 465 GLY B 1520 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 ASN A1333 CG OD1 ND2 REMARK 470 MET A1335 CG SD CE REMARK 470 ASP A1361 CG OD1 OD2 REMARK 470 LEU A1362 CG CD1 CD2 REMARK 470 GLN A1379 CG CD OE1 NE2 REMARK 470 LYS A1383 CG CD CE NZ REMARK 470 ARG A1384 CG CD NE CZ NH1 NH2 REMARK 470 LYS A1385 CG CD CE NZ REMARK 470 ARG A1412 CG CD NE CZ NH1 NH2 REMARK 470 ARG A1483 CG CD NE CZ NH1 NH2 REMARK 470 LYS A1502 CG CD CE NZ REMARK 470 LYS B1359 CG CD CE NZ REMARK 470 SER B1360 OG REMARK 470 ASP B1361 CG OD1 OD2 REMARK 470 LEU B1362 CG CD1 CD2 REMARK 470 GLN B1379 CG CD OE1 NE2 REMARK 470 ASP B1382 CG OD1 OD2 REMARK 470 ARG B1384 CG CD NE CZ NH1 NH2 REMARK 470 LYS B1385 CG CD CE NZ REMARK 470 ARG B1386 CG CD NE CZ NH1 NH2 REMARK 470 ARG B1477 CG CD NE CZ NH1 NH2 REMARK 470 LYS B1512 CG CD CE NZ REMARK 470 ILE B1513 CG1 CG2 CD1 REMARK 470 LEU B1517 CG CD1 CD2 REMARK 470 VAL B1518 CG1 CG2 REMARK 470 VAL B1519 CG1 CG2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 1477 CA CB CG CD NE CZ NH1 REMARK 480 ARG A 1477 NH2 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 THR A1357 -50.03 -122.00 REMARK 500 LYS A1358 43.02 30.87 REMARK 500 ASP A1361 -133.21 58.86 REMARK 500 LEU A1362 71.72 -117.64 REMARK 500 ARG A1384 46.70 -75.87 REMARK 500 GLN A1411 -99.21 -104.39 REMARK 500 ARG A1412 93.47 -62.04 REMARK 500 THR B1357 -102.14 64.64 REMARK 500 SER B1360 -122.92 -133.42 REMARK 500 ARG B1384 -162.53 77.30 REMARK 500 ASP B1387 85.23 62.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1813 DISTANCE = 6.14 ANGSTROMS REMARK 525 HOH A1814 DISTANCE = 6.28 ANGSTROMS REMARK 525 HOH A1815 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH A1816 DISTANCE = 7.32 ANGSTROMS REMARK 525 HOH B1823 DISTANCE = 6.31 ANGSTROMS REMARK 525 HOH B1824 DISTANCE = 6.50 ANGSTROMS 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 MG A1601 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A1348 OG1 REMARK 620 2 GDP A1602 O1B 95.1 REMARK 620 3 HOH A1717 O 173.4 90.4 REMARK 620 4 HOH A1746 O 93.1 90.6 90.3 REMARK 620 5 HOH A1758 O 87.2 176.6 87.5 86.8 REMARK 620 6 HOH B1726 O 87.1 91.7 89.3 177.7 90.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1601 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1709 O REMARK 620 2 HOH A1719 O 170.6 REMARK 620 3 THR B1348 OG1 91.8 92.2 REMARK 620 4 GDP B1602 O3B 88.5 99.5 95.8 REMARK 620 5 HOH B1758 O 88.7 83.2 85.0 177.2 REMARK 620 6 HOH B1762 O 91.2 83.3 168.5 95.4 84.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1603 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET B1409 O REMARK 620 2 TYR B1415 OH 116.1 REMARK 620 3 HOH B1731 O 102.6 140.7 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 1601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP A 1602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 1603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 1601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP B 1602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 1603 DBREF 6OJE A 1329 1520 UNP Q5S007 LRRK2_HUMAN 1329 1520 DBREF 6OJE B 1329 1520 UNP Q5S007 LRRK2_HUMAN 1329 1520 SEQADV 6OJE MET A 1315 UNP Q5S007 INITIATING METHIONINE SEQADV 6OJE GLY A 1316 UNP Q5S007 EXPRESSION TAG SEQADV 6OJE SER A 1317 UNP Q5S007 EXPRESSION TAG SEQADV 6OJE SER A 1318 UNP Q5S007 EXPRESSION TAG SEQADV 6OJE HIS A 1319 UNP Q5S007 EXPRESSION TAG SEQADV 6OJE HIS A 1320 UNP Q5S007 EXPRESSION TAG SEQADV 6OJE HIS A 1321 UNP Q5S007 EXPRESSION TAG SEQADV 6OJE HIS A 1322 UNP Q5S007 EXPRESSION TAG SEQADV 6OJE HIS A 1323 UNP Q5S007 EXPRESSION TAG SEQADV 6OJE HIS A 1324 UNP Q5S007 EXPRESSION TAG SEQADV 6OJE SER A 1325 UNP Q5S007 EXPRESSION TAG SEQADV 6OJE GLN A 1326 UNP Q5S007 EXPRESSION TAG SEQADV 6OJE ASP A 1327 UNP Q5S007 EXPRESSION TAG SEQADV 6OJE PRO A 1328 UNP Q5S007 EXPRESSION TAG SEQADV 6OJE MET B 1315 UNP Q5S007 INITIATING METHIONINE SEQADV 6OJE GLY B 1316 UNP Q5S007 EXPRESSION TAG SEQADV 6OJE SER B 1317 UNP Q5S007 EXPRESSION TAG SEQADV 6OJE SER B 1318 UNP Q5S007 EXPRESSION TAG SEQADV 6OJE HIS B 1319 UNP Q5S007 EXPRESSION TAG SEQADV 6OJE HIS B 1320 UNP Q5S007 EXPRESSION TAG SEQADV 6OJE HIS B 1321 UNP Q5S007 EXPRESSION TAG SEQADV 6OJE HIS B 1322 UNP Q5S007 EXPRESSION TAG SEQADV 6OJE HIS B 1323 UNP Q5S007 EXPRESSION TAG SEQADV 6OJE HIS B 1324 UNP Q5S007 EXPRESSION TAG SEQADV 6OJE SER B 1325 UNP Q5S007 EXPRESSION TAG SEQADV 6OJE GLN B 1326 UNP Q5S007 EXPRESSION TAG SEQADV 6OJE ASP B 1327 UNP Q5S007 EXPRESSION TAG SEQADV 6OJE PRO B 1328 UNP Q5S007 EXPRESSION TAG SEQRES 1 A 206 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER GLN ASP SEQRES 2 A 206 PRO ALA VAL PRO TYR ASN ARG MET LYS LEU MET ILE VAL SEQRES 3 A 206 GLY ASN THR GLY SER GLY LYS THR THR LEU LEU GLN GLN SEQRES 4 A 206 LEU MET LYS THR LYS LYS SER ASP LEU GLY MET GLN SER SEQRES 5 A 206 ALA THR VAL GLY ILE ASP VAL LYS ASP TRP PRO ILE GLN SEQRES 6 A 206 ILE ARG ASP LYS ARG LYS ARG ASP LEU VAL LEU ASN VAL SEQRES 7 A 206 TRP ASP PHE ALA GLY ARG GLU GLU PHE TYR SER THR HIS SEQRES 8 A 206 PRO HIS PHE MET THR GLN ARG ALA LEU TYR LEU ALA VAL SEQRES 9 A 206 TYR ASP LEU SER LYS GLY GLN ALA GLU VAL ASP ALA MET SEQRES 10 A 206 LYS PRO TRP LEU PHE ASN ILE LYS ALA ARG ALA SER SER SEQRES 11 A 206 SER PRO VAL ILE LEU VAL GLY THR HIS LEU ASP VAL SER SEQRES 12 A 206 ASP GLU LYS GLN ARG LYS ALA CYS MET SER LYS ILE THR SEQRES 13 A 206 LYS GLU LEU LEU ASN LYS ARG GLY PHE PRO ALA ILE ARG SEQRES 14 A 206 ASP TYR HIS PHE VAL ASN ALA THR GLU GLU SER ASP ALA SEQRES 15 A 206 LEU ALA LYS LEU ARG LYS THR ILE ILE ASN GLU SER LEU SEQRES 16 A 206 ASN PHE LYS ILE ARG ASP GLN LEU VAL VAL GLY SEQRES 1 B 206 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER GLN ASP SEQRES 2 B 206 PRO ALA VAL PRO TYR ASN ARG MET LYS LEU MET ILE VAL SEQRES 3 B 206 GLY ASN THR GLY SER GLY LYS THR THR LEU LEU GLN GLN SEQRES 4 B 206 LEU MET LYS THR LYS LYS SER ASP LEU GLY MET GLN SER SEQRES 5 B 206 ALA THR VAL GLY ILE ASP VAL LYS ASP TRP PRO ILE GLN SEQRES 6 B 206 ILE ARG ASP LYS ARG LYS ARG ASP LEU VAL LEU ASN VAL SEQRES 7 B 206 TRP ASP PHE ALA GLY ARG GLU GLU PHE TYR SER THR HIS SEQRES 8 B 206 PRO HIS PHE MET THR GLN ARG ALA LEU TYR LEU ALA VAL SEQRES 9 B 206 TYR ASP LEU SER LYS GLY GLN ALA GLU VAL ASP ALA MET SEQRES 10 B 206 LYS PRO TRP LEU PHE ASN ILE LYS ALA ARG ALA SER SER SEQRES 11 B 206 SER PRO VAL ILE LEU VAL GLY THR HIS LEU ASP VAL SER SEQRES 12 B 206 ASP GLU LYS GLN ARG LYS ALA CYS MET SER LYS ILE THR SEQRES 13 B 206 LYS GLU LEU LEU ASN LYS ARG GLY PHE PRO ALA ILE ARG SEQRES 14 B 206 ASP TYR HIS PHE VAL ASN ALA THR GLU GLU SER ASP ALA SEQRES 15 B 206 LEU ALA LYS LEU ARG LYS THR ILE ILE ASN GLU SER LEU SEQRES 16 B 206 ASN PHE LYS ILE ARG ASP GLN LEU VAL VAL GLY HET MG A1601 1 HET GDP A1602 28 HET MG A1603 1 HET MG B1601 1 HET GDP B1602 28 HET MG B1603 1 HETNAM MG MAGNESIUM ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 3 MG 4(MG 2+) FORMUL 4 GDP 2(C10 H15 N5 O11 P2) FORMUL 9 HOH *240(H2 O) HELIX 1 AA1 GLY A 1346 LYS A 1356 1 11 HELIX 2 AA2 GLY A 1397 SER A 1403 1 7 HELIX 3 AA3 HIS A 1405 GLN A 1411 1 7 HELIX 4 AA4 SER A 1422 GLY A 1424 5 3 HELIX 5 AA5 GLN A 1425 ALA A 1430 1 6 HELIX 6 AA6 ALA A 1430 ALA A 1442 1 13 HELIX 7 AA7 HIS A 1453 SER A 1457 5 5 HELIX 8 AA8 ASP A 1458 LEU A 1473 1 16 HELIX 9 AA9 SER A 1494 LEU A 1517 1 24 HELIX 10 AB1 GLY B 1346 THR B 1357 1 12 HELIX 11 AB2 GLY B 1397 THR B 1404 1 8 HELIX 12 AB3 HIS B 1405 ARG B 1412 1 8 HELIX 13 AB4 SER B 1422 GLY B 1424 5 3 HELIX 14 AB5 GLN B 1425 ALA B 1442 1 18 HELIX 15 AB6 HIS B 1453 SER B 1457 5 5 HELIX 16 AB7 ASP B 1458 LEU B 1473 1 16 HELIX 17 AB8 SER B 1494 ASN B 1510 1 17 HELIX 18 AB9 LYS B 1512 VAL B 1519 1 8 SHEET 1 AA1 6 ILE A1482 PHE A1487 0 SHEET 2 AA1 6 VAL A1447 THR A1452 1 N GLY A1451 O HIS A1486 SHEET 3 AA1 6 ALA A1413 ASP A1420 1 N ALA A1417 O VAL A1450 SHEET 4 AA1 6 LYS A1336 GLY A1341 1 N VAL A1340 O LEU A1416 SHEET 5 AA1 6 LEU B1388 PHE B1395 1 O TRP B1393 N ILE A1339 SHEET 6 AA1 6 ILE B1371 ILE B1378 -1 N ASP B1372 O ASP B1394 SHEET 1 AA2 6 ILE A1371 ILE A1378 0 SHEET 2 AA2 6 LEU A1388 PHE A1395 -1 O LEU A1388 N ILE A1378 SHEET 3 AA2 6 LYS B1336 VAL B1340 1 O ILE B1339 N TRP A1393 SHEET 4 AA2 6 ALA B1413 ASP B1420 1 O LEU B1414 N MET B1338 SHEET 5 AA2 6 VAL B1447 THR B1452 1 O THR B1452 N TYR B1419 SHEET 6 AA2 6 ILE B1482 PHE B1487 1 O HIS B1486 N GLY B1451 LINK OG1 THR A1348 MG MG A1601 1555 1555 2.11 LINK O MET A1409 MG MG A1603 1555 1555 2.47 LINK MG MG A1601 O1B GDP A1602 1555 1555 2.02 LINK MG MG A1601 O HOH A1717 1555 1555 2.13 LINK MG MG A1601 O HOH A1746 1555 1555 2.09 LINK MG MG A1601 O HOH A1758 1555 1555 2.09 LINK MG MG A1601 O HOH B1726 1555 1555 2.01 LINK O HOH A1709 MG MG B1601 1555 1555 2.20 LINK O HOH A1719 MG MG B1601 1555 1555 2.06 LINK OG1 THR B1348 MG MG B1601 1555 1555 2.07 LINK O MET B1409 MG MG B1603 1555 1555 2.76 LINK OH TYR B1415 MG MG B1603 1555 1555 2.61 LINK MG MG B1601 O3B GDP B1602 1555 1555 1.93 LINK MG MG B1601 O HOH B1758 1555 1555 2.04 LINK MG MG B1601 O HOH B1762 1555 1555 1.99 LINK MG MG B1603 O HOH B1731 1555 1555 2.38 SITE 1 AC1 6 THR A1348 GDP A1602 HOH A1717 HOH A1746 SITE 2 AC1 6 HOH A1758 HOH B1726 SITE 1 AC2 23 GLY A1344 SER A1345 GLY A1346 LYS A1347 SITE 2 AC2 23 THR A1348 THR A1349 HIS A1453 ASP A1455 SITE 3 AC2 23 ASN A1489 ALA A1490 MG A1601 HOH A1717 SITE 4 AC2 23 HOH A1720 HOH A1726 HOH A1736 HOH A1738 SITE 5 AC2 23 HOH A1746 PHE B1436 ASN B1437 HOH B1726 SITE 6 AC2 23 HOH B1737 HOH B1787 HOH B1817 SITE 1 AC3 3 MET A1409 ARG A1441 HOH A1702 SITE 1 AC4 7 THR A1368 HOH A1709 HOH A1719 THR B1348 SITE 2 AC4 7 GDP B1602 HOH B1758 HOH B1762 SITE 1 AC5 22 PHE A1436 ASN A1437 HOH A1709 HOH A1719 SITE 2 AC5 22 HOH A1781 GLY B1344 SER B1345 GLY B1346 SITE 3 AC5 22 LYS B1347 THR B1348 THR B1349 HIS B1453 SITE 4 AC5 22 ASP B1455 ASN B1489 ALA B1490 MG B1601 SITE 5 AC5 22 HOH B1730 HOH B1732 HOH B1743 HOH B1745 SITE 6 AC5 22 HOH B1762 HOH B1784 SITE 1 AC6 4 MET B1338 MET B1409 TYR B1415 HOH B1731 CRYST1 44.647 103.688 44.593 90.00 101.20 90.00 P 1 21 1 4 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 0.022398 0.000000 0.004435 0.00000 SCALE2 0.000000 0.009644 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022860 0.00000