PDB Short entry for 5MY9 HEADER TRANSFERASE 26-JAN-17 5MY9 TITLE CRYSTAL STRUCTURE OF HUMAN 14-3-3 SIGMA IN COMPLEX WITH LRRK2 PEPTIDE TITLE 2 PS935 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 14-3-3 PROTEIN SIGMA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: EPITHELIAL CELL MARKER PROTEIN 1,STRATIFIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: LEUCINE-RICH REPEAT SERINE/THREONINE-PROTEIN KINASE 2; COMPND 8 CHAIN: P; COMPND 9 FRAGMENT: UNP RESIDUES 929-941; COMPND 10 SYNONYM: DARDARIN; COMPND 11 EC: 2.7.11.1; COMPND 12 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: SFN, HME1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS 14-3-3 LRRK2 PHOSPHORYLATION PPI, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR L.M.STEVERS,R.M.J.M.DE VRIES,C.OTTMANN REVDAT 3 17-JAN-24 5MY9 1 LINK REVDAT 2 05-APR-17 5MY9 1 JRNL REVDAT 1 01-MAR-17 5MY9 0 JRNL AUTH L.M.STEVERS,R.M.DE VRIES,R.G.DOVESTON,L.G.MILROY, JRNL AUTH 2 L.BRUNSVELD,C.OTTMANN JRNL TITL STRUCTURAL INTERFACE BETWEEN LRRK2 AND 14-3-3 PROTEIN. JRNL REF BIOCHEM. J. V. 474 1273 2017 JRNL REFN ESSN 1470-8728 JRNL PMID 28202711 JRNL DOI 10.1042/BCJ20161078 REMARK 2 REMARK 2 RESOLUTION. 1.33 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11_2567: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.290 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 128449 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 6426 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 45.4849 - 4.1217 1.00 4094 211 0.1761 0.1823 REMARK 3 2 4.1217 - 3.2718 1.00 4113 214 0.1488 0.1690 REMARK 3 3 3.2718 - 2.8583 1.00 4080 219 0.1654 0.1719 REMARK 3 4 2.8583 - 2.5970 1.00 4050 211 0.1739 0.2057 REMARK 3 5 2.5970 - 2.4109 1.00 4122 214 0.1677 0.1763 REMARK 3 6 2.4109 - 2.2687 1.00 4072 213 0.1538 0.1520 REMARK 3 7 2.2687 - 2.1551 1.00 4098 214 0.1555 0.1727 REMARK 3 8 2.1551 - 2.0613 1.00 4113 213 0.1582 0.1662 REMARK 3 9 2.0613 - 1.9820 1.00 4062 215 0.1577 0.1545 REMARK 3 10 1.9820 - 1.9136 1.00 4077 214 0.1586 0.1767 REMARK 3 11 1.9136 - 1.8537 1.00 4117 217 0.1679 0.1914 REMARK 3 12 1.8537 - 1.8007 1.00 4079 216 0.1706 0.1948 REMARK 3 13 1.8007 - 1.7533 1.00 4062 211 0.1899 0.1885 REMARK 3 14 1.7533 - 1.7106 1.00 4109 217 0.1848 0.2041 REMARK 3 15 1.7106 - 1.6717 1.00 4093 208 0.1989 0.2608 REMARK 3 16 1.6717 - 1.6361 1.00 4075 219 0.2078 0.2198 REMARK 3 17 1.6361 - 1.6034 1.00 4042 217 0.2374 0.2904 REMARK 3 18 1.6034 - 1.5731 1.00 4094 216 0.2473 0.2708 REMARK 3 19 1.5731 - 1.5450 1.00 4083 220 0.2601 0.2981 REMARK 3 20 1.5450 - 1.5188 1.00 4110 215 0.2799 0.2792 REMARK 3 21 1.5188 - 1.4943 1.00 4069 216 0.2799 0.2387 REMARK 3 22 1.4943 - 1.4713 1.00 4061 218 0.2827 0.3009 REMARK 3 23 1.4713 - 1.4497 1.00 4080 216 0.2842 0.2990 REMARK 3 24 1.4497 - 1.4293 1.00 4144 219 0.2874 0.2881 REMARK 3 25 1.4293 - 1.4099 1.00 4059 217 0.2884 0.3029 REMARK 3 26 1.4099 - 1.3916 1.00 4071 210 0.2989 0.3210 REMARK 3 27 1.3916 - 1.3742 1.00 4036 216 0.3022 0.3421 REMARK 3 28 1.3742 - 1.3577 1.00 4079 218 0.3228 0.3239 REMARK 3 29 1.3577 - 1.3419 1.00 4120 217 0.3259 0.3317 REMARK 3 30 1.3419 - 1.3268 0.87 3559 185 0.3865 0.3692 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.380 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.007 2042 REMARK 3 ANGLE : 0.820 2772 REMARK 3 CHIRALITY : 0.064 302 REMARK 3 PLANARITY : 0.004 364 REMARK 3 DIHEDRAL : 17.341 818 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5MY9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1200003226. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9786 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 380505 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.088 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.9600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 11.70 REMARK 200 R MERGE FOR SHELL (I) : 0.90900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.11 2567 REMARK 200 STARTING MODEL: 5BTV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES, NACL, DTT, PH 7.4, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 31.21500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.21500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 41.14550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 56.01500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 41.14550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 56.01500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 31.21500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 41.14550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 56.01500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 31.21500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 41.14550 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 56.01500 REMARK 290 SMTRY3 8 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, P 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 APPLY THE FOLLOWING TO CHAINS: A, P REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 CA CA A 303 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 LEU P 929 REMARK 465 GLN P 930 REMARK 465 ARG P 931 REMARK 465 HIS P 932 REMARK 465 GLY P 937 REMARK 465 PRO P 938 REMARK 465 ILE P 939 REMARK 465 PHE P 940 REMARK 465 ASP P 941 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 HOH A 535 O HOH A 624 1.49 REMARK 500 O HOH A 640 O HOH A 655 1.68 REMARK 500 O HOH A 760 O HOH P 1010 1.92 REMARK 500 O HOH A 409 O HOH A 413 1.92 REMARK 500 O HOH A 649 O HOH A 658 1.93 REMARK 500 O HOH A 575 O HOH A 621 1.95 REMARK 500 O HOH A 438 O HOH A 665 1.96 REMARK 500 O HOH A 742 O HOH A 772 1.98 REMARK 500 O HOH A 495 O HOH A 711 2.00 REMARK 500 O HOH A 510 O HOH A 734 2.01 REMARK 500 O HOH A 718 O HOH A 765 2.01 REMARK 500 O HOH A 539 O HOH A 557 2.03 REMARK 500 O HOH A 573 O HOH A 602 2.03 REMARK 500 O HOH A 536 O HOH A 646 2.03 REMARK 500 O HOH A 740 O HOH A 773 2.03 REMARK 500 O HOH A 647 O HOH A 676 2.05 REMARK 500 O HOH A 413 O HOH A 460 2.07 REMARK 500 O HOH A 700 O HOH A 703 2.07 REMARK 500 O HOH A 427 O HOH A 539 2.11 REMARK 500 O HOH A 416 O HOH A 574 2.11 REMARK 500 O HOH A 620 O HOH A 671 2.13 REMARK 500 O HOH A 659 O HOH A 691 2.14 REMARK 500 O HOH A 618 O HOH A 652 2.17 REMARK 500 O HOH P 1001 O HOH P 1003 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 652 O HOH A 652 3454 1.90 REMARK 500 O HOH A 771 O HOH A 771 3455 1.95 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 ARG A 18 76.51 -106.36 REMARK 500 HIS A 106 38.93 -144.52 REMARK 500 THR A 136 -7.64 -142.91 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 A 772 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH A 773 DISTANCE = 6.28 ANGSTROMS REMARK 525 HOH P1010 DISTANCE = 6.28 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 CA A 303 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 2 OE1 REMARK 620 2 GLU A 2 OE1 0.0 REMARK 620 3 HOH A 444 O 76.6 76.6 REMARK 620 4 HOH A 444 O 82.6 82.6 150.9 REMARK 620 5 HOH A 640 O 84.1 84.1 126.6 70.1 REMARK 620 6 HOH A 640 O 146.4 146.4 70.1 126.5 119.1 REMARK 620 7 HOH A 655 O 81.2 81.2 88.1 108.6 39.4 101.2 REMARK 620 8 HOH A 655 O 167.0 167.0 108.6 88.1 101.2 39.4 110.5 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 35 OE1 REMARK 620 2 GLU A 35 OE2 50.8 REMARK 620 3 GLU A 110 O 83.6 86.3 REMARK 620 4 GLU A 188 OE2 85.5 120.2 45.1 REMARK 620 5 HOH A 485 O 132.4 82.0 88.2 119.8 REMARK 620 6 HOH A 562 O 144.2 160.5 105.8 78.3 83.1 REMARK 620 7 HOH A 641 O 89.7 82.9 169.2 142.9 90.1 84.6 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 75 OE1 REMARK 620 2 GLU A 161 O 68.3 REMARK 620 3 HOH A 497 O 67.4 1.0 REMARK 620 4 HOH A 550 O 67.9 2.8 3.3 REMARK 620 5 HOH A 637 O 65.9 2.7 2.2 2.6 REMARK 620 6 HOH A 650 O 66.7 3.2 3.3 1.2 1.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 304 DBREF 5MY9 A 1 231 UNP P31947 1433S_HUMAN 1 231 DBREF 5MY9 P 929 941 UNP Q5S007 LRRK2_HUMAN 929 941 SEQADV 5MY9 GLY A -4 UNP P31947 EXPRESSION TAG SEQADV 5MY9 ALA A -3 UNP P31947 EXPRESSION TAG SEQADV 5MY9 MET A -2 UNP P31947 EXPRESSION TAG SEQADV 5MY9 GLY A -1 UNP P31947 EXPRESSION TAG SEQADV 5MY9 SER A 0 UNP P31947 EXPRESSION TAG SEQRES 1 A 236 GLY ALA MET GLY SER MET GLU ARG ALA SER LEU ILE GLN SEQRES 2 A 236 LYS ALA LYS LEU ALA GLU GLN ALA GLU ARG TYR GLU ASP SEQRES 3 A 236 MET ALA ALA PHE MET LYS GLY ALA VAL GLU LYS GLY GLU SEQRES 4 A 236 GLU LEU SER CYS GLU GLU ARG ASN LEU LEU SER VAL ALA SEQRES 5 A 236 TYR LYS ASN VAL VAL GLY GLY GLN ARG ALA ALA TRP ARG SEQRES 6 A 236 VAL LEU SER SER ILE GLU GLN LYS SER ASN GLU GLU GLY SEQRES 7 A 236 SER GLU GLU LYS GLY PRO GLU VAL ARG GLU TYR ARG GLU SEQRES 8 A 236 LYS VAL GLU THR GLU LEU GLN GLY VAL CYS ASP THR VAL SEQRES 9 A 236 LEU GLY LEU LEU ASP SER HIS LEU ILE LYS GLU ALA GLY SEQRES 10 A 236 ASP ALA GLU SER ARG VAL PHE TYR LEU LYS MET LYS GLY SEQRES 11 A 236 ASP TYR TYR ARG TYR LEU ALA GLU VAL ALA THR GLY ASP SEQRES 12 A 236 ASP LYS LYS ARG ILE ILE ASP SER ALA ARG SER ALA TYR SEQRES 13 A 236 GLN GLU ALA MET ASP ILE SER LYS LYS GLU MET PRO PRO SEQRES 14 A 236 THR ASN PRO ILE ARG LEU GLY LEU ALA LEU ASN PHE SER SEQRES 15 A 236 VAL PHE HIS TYR GLU ILE ALA ASN SER PRO GLU GLU ALA SEQRES 16 A 236 ILE SER LEU ALA LYS THR THR PHE ASP GLU ALA MET ALA SEQRES 17 A 236 ASP LEU HIS THR LEU SER GLU ASP SER TYR LYS ASP SER SEQRES 18 A 236 THR LEU ILE MET GLN LEU LEU ARG ASP ASN LEU THR LEU SEQRES 19 A 236 TRP THR SEQRES 1 P 13 LEU GLN ARG HIS SER ASN SEP LEU GLY PRO ILE PHE ASP MODRES 5MY9 SEP P 935 SER MODIFIED RESIDUE HET SEP P 935 10 HET CA A 301 1 HET CA A 302 1 HET CA A 303 1 HET CL A 304 1 HETNAM SEP PHOSPHOSERINE HETNAM CA CALCIUM ION HETNAM CL CHLORIDE ION HETSYN SEP PHOSPHONOSERINE FORMUL 2 SEP C3 H8 N O6 P FORMUL 3 CA 3(CA 2+) FORMUL 6 CL CL 1- FORMUL 7 HOH *383(H2 O) HELIX 1 AA1 GLU A 2 ALA A 16 1 15 HELIX 2 AA2 ARG A 18 GLU A 31 1 14 HELIX 3 AA3 SER A 37 SER A 69 1 33 HELIX 4 AA4 PRO A 79 SER A 105 1 27 HELIX 5 AA5 HIS A 106 ALA A 111 1 6 HELIX 6 AA6 ASP A 113 ALA A 135 1 23 HELIX 7 AA7 ASP A 139 MET A 162 1 24 HELIX 8 AA8 ASN A 166 ILE A 183 1 18 HELIX 9 AA9 SER A 186 ALA A 203 1 18 HELIX 10 AB1 ASP A 204 LEU A 208 5 5 HELIX 11 AB2 SER A 209 THR A 231 1 23 LINK C ASN P 934 N SEP P 935 1555 1555 1.33 LINK C SEP P 935 N LEU P 936 1555 1555 1.33 LINK OE1 GLU A 2 CA CA A 303 1555 1555 2.40 LINK OE1 GLU A 2 CA CA A 303 1555 3454 2.40 LINK OE1 GLU A 35 CA CA A 302 1555 1555 2.70 LINK OE2 GLU A 35 CA CA A 302 1555 1555 2.34 LINK OE1 GLU A 75 CA CA A 301 1555 7455 2.56 LINK O GLU A 110 CA CA A 302 1555 1555 2.29 LINK O GLU A 161 CA CA A 301 1555 1555 2.27 LINK OE2 GLU A 188 CA CA A 302 1555 6445 2.37 LINK CA CA A 301 O HOH A 497 1555 7445 2.36 LINK CA CA A 301 O HOH A 550 1555 1555 2.57 LINK CA CA A 301 O HOH A 637 1555 1555 2.35 LINK CA CA A 301 O HOH A 650 1555 6444 2.38 LINK CA CA A 302 O HOH A 485 1555 1555 2.32 LINK CA CA A 302 O HOH A 562 1555 6444 2.42 LINK CA CA A 302 O HOH A 641 1555 1555 2.38 LINK CA CA A 303 O HOH A 444 1555 1555 2.53 LINK CA CA A 303 O HOH A 444 1555 3454 2.53 LINK CA CA A 303 O HOH A 640 1555 1555 2.25 LINK CA CA A 303 O HOH A 640 1555 3454 2.26 LINK CA CA A 303 O HOH A 655 1555 1555 2.61 LINK CA CA A 303 O HOH A 655 1555 3454 2.62 CISPEP 1 SER A 105 HIS A 106 0 5.99 SITE 1 AC1 6 GLU A 75 GLU A 161 HOH A 497 HOH A 550 SITE 2 AC1 6 HOH A 637 HOH A 650 SITE 1 AC2 6 GLU A 35 GLU A 110 GLU A 188 HOH A 485 SITE 2 AC2 6 HOH A 562 HOH A 641 SITE 1 AC3 4 GLU A 2 HOH A 444 HOH A 640 HOH A 655 SITE 1 AC4 2 LYS A 9 HOH A 717 CRYST1 82.291 112.030 62.430 90.00 90.00 90.00 C 2 2 21 8 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 0.012152 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008926 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016018 0.00000