PDB Short entry for 3D6T HEADER TRANSFERASE 20-MAY-08 3D6T TITLE STRUCTURE OF THE ROC DOMAIN FROM THE PARKINSON'S DISEASE-ASSOCIATED TITLE 2 LEUCINE-RICH REPEAT KINASE 2 REVEALS A DIMERIC GTPASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEUCINE-RICH REPEAT SERINE/THREONINE-PROTEIN KINASE 2; COMPND 3 CHAIN: B; COMPND 4 FRAGMENT: MIRO DOMAIN; COMPND 5 SYNONYM: DARDARIN; 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21GOLDDE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PSKB3 KEYWDS PARKINSON'S DISEASE, LRRK2, ROC, ROCO, GTPASE, KINASE, ATP-BINDING, KEYWDS 2 DISEASE MUTATION, GTP-BINDING, GTPASE ACTIVATION, LEUCINE-RICH KEYWDS 3 REPEAT, MEMBRANE, NUCLEOTIDE-BINDING, PARKINSON DISEASE, KEYWDS 4 SERINE/THREONINE-PROTEIN KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.DENG REVDAT 5 28-FEB-18 3D6T 1 KEYWDS REVDAT 4 25-OCT-17 3D6T 1 SOURCE REMARK REVDAT 3 13-JUL-11 3D6T 1 VERSN REVDAT 2 24-FEB-09 3D6T 1 VERSN REVDAT 1 10-JUN-08 3D6T 0 JRNL AUTH J.DENG,P.A.LEWIS,E.GREGGIO,E.SLUCH,A.BEILINA,M.R.COOKSON JRNL TITL STRUCTURE OF THE ROC DOMAIN FROM THE PARKINSON'S JRNL TITL 2 DISEASE-ASSOCIATED LEUCINE-RICH REPEAT KINASE 2 REVEALS A JRNL TITL 3 DIMERIC GTPASE JRNL REF PROC.NATL.ACAD.SCI.USA V. 105 1499 2008 JRNL REFN ISSN 0027-8424 JRNL PMID 18230735 JRNL DOI 10.1073/PNAS.0709098105 REMARK 2 REMARK 2 RESOLUTION. 2.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.09 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 3 NUMBER OF REFLECTIONS : 5109 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.307 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.500 REMARK 3 FREE R VALUE TEST SET COUNT : 230 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) : 2.43 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.50 REMARK 3 REFLECTION IN BIN (WORKING SET) : 238 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 65.21 REMARK 3 BIN R VALUE (WORKING SET) : 0.3040 REMARK 3 BIN FREE R VALUE SET COUNT : 15 REMARK 3 BIN FREE R VALUE : 0.5410 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 994 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 6 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.08000 REMARK 3 B22 (A**2) : -0.48000 REMARK 3 B33 (A**2) : 0.59000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.04000 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): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.288 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 25.808 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.861 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1023 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1383 ; 2.342 ; 1.995 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 116 ; 8.302 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 38 ;34.602 ;22.895 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 168 ;20.902 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;14.390 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 161 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 717 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 378 ; 0.290 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 667 ; 0.339 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 31 ; 0.187 ; 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): 46 ; 0.228 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.256 ; 0.200 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): 633 ; 0.887 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 977 ; 1.419 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 467 ; 2.300 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 406 ; 3.375 ; 4.500 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): NULL ; NULL ; NULL 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 : 13 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 : B 1335 B 1339 REMARK 3 ORIGIN FOR THE GROUP (A): 31.8868 -8.7054 29.0090 REMARK 3 T TENSOR REMARK 3 T11: 0.1118 T22: 0.0893 REMARK 3 T33: 0.1758 T12: -0.0770 REMARK 3 T13: 0.0104 T23: -0.1423 REMARK 3 L TENSOR REMARK 3 L11: 38.3732 L22: 20.8940 REMARK 3 L33: 5.8073 L12: -16.6866 REMARK 3 L13: -7.1720 L23: -4.6862 REMARK 3 S TENSOR REMARK 3 S11: 0.2686 S12: -1.1778 S13: 0.1584 REMARK 3 S21: 0.5322 S22: 0.0198 S23: 0.5494 REMARK 3 S31: -1.0741 S32: 0.0109 S33: -0.2883 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 1340 B 1351 REMARK 3 ORIGIN FOR THE GROUP (A): 41.1984 -16.0176 23.8143 REMARK 3 T TENSOR REMARK 3 T11: 0.1221 T22: 0.1616 REMARK 3 T33: 0.1328 T12: 0.0528 REMARK 3 T13: 0.0214 T23: -0.0577 REMARK 3 L TENSOR REMARK 3 L11: 7.6445 L22: 11.5705 REMARK 3 L33: 0.3873 L12: -3.7280 REMARK 3 L13: 1.4435 L23: 0.3536 REMARK 3 S TENSOR REMARK 3 S11: 0.0241 S12: 0.0897 S13: -0.0192 REMARK 3 S21: 0.1579 S22: -0.1615 S23: -0.2721 REMARK 3 S31: -0.3169 S32: -0.0116 S33: 0.1374 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1353 B 1390 REMARK 3 ORIGIN FOR THE GROUP (A): 30.1860 -16.4987 30.5170 REMARK 3 T TENSOR REMARK 3 T11: 0.1057 T22: 0.1335 REMARK 3 T33: 0.1782 T12: 0.0213 REMARK 3 T13: 0.1652 T23: 0.0396 REMARK 3 L TENSOR REMARK 3 L11: 3.7869 L22: 5.6450 REMARK 3 L33: 7.5350 L12: -0.7385 REMARK 3 L13: 5.2293 L23: 0.2940 REMARK 3 S TENSOR REMARK 3 S11: -0.2819 S12: -0.2808 S13: -0.3533 REMARK 3 S21: 0.7605 S22: 0.1847 S23: 0.7599 REMARK 3 S31: 0.0723 S32: -0.7128 S33: 0.0972 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1392 B 1396 REMARK 3 ORIGIN FOR THE GROUP (A): 32.6690 -12.4144 22.9618 REMARK 3 T TENSOR REMARK 3 T11: 0.0631 T22: 0.1963 REMARK 3 T33: 0.1661 T12: -0.0681 REMARK 3 T13: 0.0445 T23: -0.0653 REMARK 3 L TENSOR REMARK 3 L11: 10.2691 L22: 5.4351 REMARK 3 L33: 15.3384 L12: 7.4708 REMARK 3 L13: -12.5504 L23: -9.1304 REMARK 3 S TENSOR REMARK 3 S11: -0.2125 S12: -0.4444 S13: -1.2122 REMARK 3 S21: 0.1242 S22: -0.4085 S23: 0.3411 REMARK 3 S31: -0.2207 S32: 0.3468 S33: 0.6210 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1397 B 1401 REMARK 3 ORIGIN FOR THE GROUP (A): 37.4677 -7.9255 15.4981 REMARK 3 T TENSOR REMARK 3 T11: 0.0486 T22: 0.1514 REMARK 3 T33: 0.1717 T12: 0.0168 REMARK 3 T13: 0.1059 T23: -0.0121 REMARK 3 L TENSOR REMARK 3 L11: 13.6589 L22: 29.3068 REMARK 3 L33: 52.7257 L12: 4.5987 REMARK 3 L13: -7.1223 L23: 34.4869 REMARK 3 S TENSOR REMARK 3 S11: 0.1925 S12: 1.5941 S13: 0.9887 REMARK 3 S21: -1.4705 S22: 1.2153 S23: -1.4178 REMARK 3 S31: -1.2512 S32: 1.3216 S33: -1.4078 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1402 B 1407 REMARK 3 ORIGIN FOR THE GROUP (A): 31.3894 -1.2524 14.7079 REMARK 3 T TENSOR REMARK 3 T11: 0.0416 T22: 0.0776 REMARK 3 T33: 0.2312 T12: -0.0113 REMARK 3 T13: 0.0176 T23: 0.0817 REMARK 3 L TENSOR REMARK 3 L11: 5.6023 L22: 18.4098 REMARK 3 L33: 4.3829 L12: -4.1697 REMARK 3 L13: 3.7903 L23: 2.4548 REMARK 3 S TENSOR REMARK 3 S11: -0.0631 S12: 0.2440 S13: 0.6438 REMARK 3 S21: 0.5860 S22: 0.0168 S23: 0.1029 REMARK 3 S31: 0.3653 S32: -0.4653 S33: 0.0463 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1408 B 1414 REMARK 3 ORIGIN FOR THE GROUP (A): 24.5734 -1.2527 10.8083 REMARK 3 T TENSOR REMARK 3 T11: 0.0818 T22: 0.0846 REMARK 3 T33: 0.3090 T12: 0.0074 REMARK 3 T13: 0.0071 T23: 0.0778 REMARK 3 L TENSOR REMARK 3 L11: 15.5813 L22: 5.6768 REMARK 3 L33: 7.4130 L12: 9.2808 REMARK 3 L13: 3.6538 L23: 3.1644 REMARK 3 S TENSOR REMARK 3 S11: -0.6225 S12: 0.2553 S13: 0.7466 REMARK 3 S21: -0.3679 S22: -0.1582 S23: 0.5295 REMARK 3 S31: -0.4182 S32: 0.6056 S33: 0.7807 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1415 B 1422 REMARK 3 ORIGIN FOR THE GROUP (A): 7.6025 -11.2514 12.5676 REMARK 3 T TENSOR REMARK 3 T11: 0.1135 T22: 0.1239 REMARK 3 T33: 0.1518 T12: -0.0279 REMARK 3 T13: -0.0154 T23: 0.0063 REMARK 3 L TENSOR REMARK 3 L11: 10.5949 L22: 4.8580 REMARK 3 L33: 0.7387 L12: 2.4215 REMARK 3 L13: 0.9096 L23: 1.8942 REMARK 3 S TENSOR REMARK 3 S11: 0.3534 S12: 0.1070 S13: 0.7371 REMARK 3 S21: 0.0335 S22: -0.2262 S23: 0.9263 REMARK 3 S31: 0.1043 S32: -0.0470 S33: -0.1272 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1423 B 1433 REMARK 3 ORIGIN FOR THE GROUP (A): 2.0613 -6.2718 17.5588 REMARK 3 T TENSOR REMARK 3 T11: 0.0884 T22: 0.0420 REMARK 3 T33: 0.3527 T12: 0.0064 REMARK 3 T13: 0.1341 T23: -0.0693 REMARK 3 L TENSOR REMARK 3 L11: 3.7623 L22: 20.0070 REMARK 3 L33: 9.1305 L12: 7.9333 REMARK 3 L13: -2.8394 L23: -1.2007 REMARK 3 S TENSOR REMARK 3 S11: -0.4019 S12: 0.7914 S13: -0.4284 REMARK 3 S21: -0.4656 S22: 0.2923 S23: 0.5799 REMARK 3 S31: 0.3732 S32: -0.3494 S33: 0.1096 REMARK 3 REMARK 3 TLS GROUP : 10 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1434 B 1453 REMARK 3 ORIGIN FOR THE GROUP (A): 11.9260 -3.1616 13.0041 REMARK 3 T TENSOR REMARK 3 T11: 0.0768 T22: 0.0926 REMARK 3 T33: 0.1558 T12: 0.0137 REMARK 3 T13: -0.0002 T23: 0.0592 REMARK 3 L TENSOR REMARK 3 L11: 1.6847 L22: 5.1109 REMARK 3 L33: 3.4996 L12: 0.7692 REMARK 3 L13: -0.0131 L23: 1.1492 REMARK 3 S TENSOR REMARK 3 S11: 0.0068 S12: 0.1465 S13: 0.4700 REMARK 3 S21: -0.3266 S22: 0.1610 S23: 0.0995 REMARK 3 S31: -0.3348 S32: -0.2177 S33: -0.1678 REMARK 3 REMARK 3 TLS GROUP : 11 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1454 B 1474 REMARK 3 ORIGIN FOR THE GROUP (A): -1.0441 -11.3989 9.2270 REMARK 3 T TENSOR REMARK 3 T11: 0.0932 T22: 0.0622 REMARK 3 T33: 0.1655 T12: -0.0057 REMARK 3 T13: -0.0008 T23: -0.0089 REMARK 3 L TENSOR REMARK 3 L11: 8.4947 L22: 12.1332 REMARK 3 L33: 4.9460 L12: 9.7723 REMARK 3 L13: 4.0049 L23: 6.2581 REMARK 3 S TENSOR REMARK 3 S11: -0.2981 S12: -0.2316 S13: 0.6055 REMARK 3 S21: -1.4781 S22: 0.1661 S23: 1.8460 REMARK 3 S31: -0.6227 S32: -0.4752 S33: 0.1320 REMARK 3 REMARK 3 TLS GROUP : 12 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1478 B 1486 REMARK 3 ORIGIN FOR THE GROUP (A): 8.4244 -2.7430 5.7705 REMARK 3 T TENSOR REMARK 3 T11: -0.0002 T22: 0.0721 REMARK 3 T33: 0.2085 T12: -0.1017 REMARK 3 T13: -0.1351 T23: 0.1104 REMARK 3 L TENSOR REMARK 3 L11: 5.4349 L22: 13.8121 REMARK 3 L33: 9.2836 L12: -1.0352 REMARK 3 L13: -2.6307 L23: -0.1045 REMARK 3 S TENSOR REMARK 3 S11: -0.3587 S12: 0.8004 S13: 0.1447 REMARK 3 S21: -1.5163 S22: 0.2468 S23: 0.3236 REMARK 3 S31: -0.5531 S32: -0.5203 S33: 0.1119 REMARK 3 REMARK 3 TLS GROUP : 13 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1487 B 1505 REMARK 3 ORIGIN FOR THE GROUP (A): 10.9963 -17.4201 2.8060 REMARK 3 T TENSOR REMARK 3 T11: 0.2764 T22: 0.0443 REMARK 3 T33: -0.0248 T12: 0.0114 REMARK 3 T13: -0.0350 T23: -0.0365 REMARK 3 L TENSOR REMARK 3 L11: 10.4482 L22: 5.1334 REMARK 3 L33: 3.7085 L12: 3.3272 REMARK 3 L13: -1.7694 L23: 0.3176 REMARK 3 S TENSOR REMARK 3 S11: -0.3721 S12: 0.7620 S13: -0.4408 REMARK 3 S21: -1.0271 S22: 0.1653 S23: -0.1497 REMARK 3 S31: 0.3710 S32: -0.2961 S33: 0.2068 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3D6T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAY-08. REMARK 100 THE DEPOSITION ID IS D_1000047664. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-07 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97926 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5109 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.430 REMARK 200 RESOLUTION RANGE LOW (A) : 21.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4000, 100MM MGCL2, 0.1M TRIS, REMARK 280 5MM GTP, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 34.95950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.58350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 34.95950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.58350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 53.38564 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 39.40830 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 GLN B 1352 REMARK 465 LYS B 1356 REMARK 465 THR B 1357 REMARK 465 LYS B 1358 REMARK 465 LYS B 1359 REMARK 465 SER B 1360 REMARK 465 ASP B 1361 REMARK 465 LEU B 1362 REMARK 465 GLY B 1363 REMARK 465 MSE B 1364 REMARK 465 GLN B 1365 REMARK 465 SER B 1366 REMARK 465 ALA B 1367 REMARK 465 THR B 1368 REMARK 465 VAL B 1369 REMARK 465 ILE B 1378 REMARK 465 GLN B 1379 REMARK 465 ILE B 1380 REMARK 465 ARG B 1381 REMARK 465 ASP B 1382 REMARK 465 LYS B 1383 REMARK 465 ARG B 1384 REMARK 465 LYS B 1385 REMARK 465 ARG B 1386 REMARK 465 ASP B 1387 REMARK 465 ASN B 1391 REMARK 465 GLU B 1459 REMARK 465 LYS B 1460 REMARK 465 GLN B 1461 REMARK 465 ARG B 1462 REMARK 465 LYS B 1463 REMARK 465 ALA B 1464 REMARK 465 CYS B 1465 REMARK 465 MSE B 1466 REMARK 465 SER B 1467 REMARK 465 THR B 1470 REMARK 465 LYS B 1471 REMARK 465 GLU B 1472 REMARK 465 ASN B 1475 REMARK 465 LYS B 1476 REMARK 465 ARG B 1477 REMARK 465 ASP B 1495 REMARK 465 ALA B 1496 REMARK 465 LEU B 1497 REMARK 465 ALA B 1498 REMARK 465 LYS B 1499 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 GLN B 1353 CG REMARK 480 ASP B 1375 CB CG OD1 OD2 REMARK 480 ARG B 1398 CG CD NE REMARK 480 GLU B 1399 CG CD OE1 OE2 REMARK 480 GLN B 1411 CB CG REMARK 480 ARG B 1412 CD REMARK 480 LYS B 1423 CG CD CE NZ REMARK 480 GLN B 1425 CB CG CD OE1 NE2 REMARK 480 GLU B 1427 CG CD OE1 OE2 REMARK 480 ASP B 1429 OD1 OD2 REMARK 480 SER B 1444 CB OG REMARK 480 ARG B 1483 CB CG REMARK 480 GLU B 1493 CB CG REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP B 1 DBREF 3D6T B 1336 1505 UNP Q5S007 LRRK2_HUMAN 1336 1505 SEQADV 3D6T MSE B 1335 UNP Q5S007 INITIATING METHIONINE SEQRES 1 B 171 MSE LYS LEU MSE ILE VAL GLY ASN THR GLY SER GLY LYS SEQRES 2 B 171 THR THR LEU LEU GLN GLN LEU MSE LYS THR LYS LYS SER SEQRES 3 B 171 ASP LEU GLY MSE GLN SER ALA THR VAL GLY ILE ASP VAL SEQRES 4 B 171 LYS ASP TRP PRO ILE GLN ILE ARG ASP LYS ARG LYS ARG SEQRES 5 B 171 ASP LEU VAL LEU ASN VAL TRP ASP PHE ALA GLY ARG GLU SEQRES 6 B 171 GLU PHE TYR SER THR HIS PRO HIS PHE MSE THR GLN ARG SEQRES 7 B 171 ALA LEU TYR LEU ALA VAL TYR ASP LEU SER LYS GLY GLN SEQRES 8 B 171 ALA GLU VAL ASP ALA MSE LYS PRO TRP LEU PHE ASN ILE SEQRES 9 B 171 LYS ALA ARG ALA SER SER SER PRO VAL ILE LEU VAL GLY SEQRES 10 B 171 THR HIS LEU ASP VAL SER ASP GLU LYS GLN ARG LYS ALA SEQRES 11 B 171 CYS MSE SER LYS ILE THR LYS GLU LEU LEU ASN LYS ARG SEQRES 12 B 171 GLY PHE PRO ALA ILE ARG ASP TYR HIS PHE VAL ASN ALA SEQRES 13 B 171 THR GLU GLU SER ASP ALA LEU ALA LYS LEU ARG LYS THR SEQRES 14 B 171 ILE ILE MODRES 3D6T MSE B 1335 MET SELENOMETHIONINE MODRES 3D6T MSE B 1338 MET SELENOMETHIONINE MODRES 3D6T MSE B 1355 MET SELENOMETHIONINE MODRES 3D6T MSE B 1409 MET SELENOMETHIONINE MODRES 3D6T MSE B 1431 MET SELENOMETHIONINE HET MSE B1335 8 HET MSE B1338 8 HET MSE B1355 8 HET MSE B1409 8 HET MSE B1431 8 HET MG B 2 1 HET GDP B 1 28 HETNAM MSE SELENOMETHIONINE HETNAM MG MAGNESIUM ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 1 MSE 5(C5 H11 N O2 SE) FORMUL 2 MG MG 2+ FORMUL 3 GDP C10 H15 N5 O11 P2 FORMUL 4 HOH *6(H2 O) HELIX 1 1 GLY B 1346 LEU B 1351 1 6 HELIX 2 2 GLY B 1397 SER B 1403 1 7 HELIX 3 3 HIS B 1405 ARG B 1412 1 8 HELIX 4 4 MSE B 1431 ALA B 1442 1 12 SHEET 1 A 3 MSE B1338 ILE B1339 0 SHEET 2 A 3 TRP B1393 PHE B1395 1 O TRP B1393 N ILE B1339 SHEET 3 A 3 ILE B1371 VAL B1373 -1 N ASP B1372 O ASP B1394 SHEET 1 B 3 TYR B1415 ASP B1420 0 SHEET 2 B 3 PRO B1446 THR B1452 1 O VAL B1450 N TYR B1419 SHEET 3 B 3 ALA B1481 PHE B1487 1 O HIS B1486 N LEU B1449 LINK C MSE B1335 N LYS B1336 1555 1555 1.32 LINK C LEU B1337 N MSE B1338 1555 1555 1.33 LINK C MSE B1338 N ILE B1339 1555 1555 1.30 LINK C LEU B1354 N MSE B1355 1555 1555 1.31 LINK C PHE B1408 N MSE B1409 1555 1555 1.34 LINK C MSE B1409 N THR B1410 1555 1555 1.34 LINK C ALA B1430 N MSE B1431 1555 1555 1.33 LINK C MSE B1431 N LYS B1432 1555 1555 1.33 LINK MG MG B 2 O2B GDP B 1 1555 1555 2.17 SITE 1 AC1 1 THR B1348 SITE 1 AC2 14 GLY B1344 SER B1345 GLY B1346 LYS B1347 SITE 2 AC2 14 THR B1348 THR B1349 TYR B1402 PRO B1433 SITE 3 AC2 14 PHE B1436 ASN B1437 HIS B1453 ASP B1455 SITE 4 AC2 14 ASN B1489 ALA B1490 CRYST1 69.919 53.167 42.736 90.00 112.76 90.00 C 1 2 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 0.014302 0.000000 0.006000 0.00000 SCALE2 0.000000 0.018809 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025375 0.00000 HETATM 1 N MSE B1335 25.523 -6.804 33.344 1.00 35.12 N HETATM 2 CA MSE B1335 26.702 -6.128 32.699 1.00 35.99 C HETATM 3 C MSE B1335 27.568 -7.104 31.915 1.00 34.03 C HETATM 4 O MSE B1335 27.473 -8.308 32.103 1.00 34.94 O HETATM 5 CB MSE B1335 27.583 -5.424 33.735 1.00 36.20 C HETATM 6 CG MSE B1335 28.013 -6.299 34.928 1.00 38.25 C HETATM 7 SE MSE B1335 29.882 -6.039 35.507 1.00 41.28 SE HETATM 8 CE MSE B1335 30.817 -6.951 34.069 1.00 38.68 C