HEADER SIGNALING PROTEIN 19-AUG-18 6HDU TITLE CRYSTAL STRUCTURE OF HUMAN RAB38 IN COMPLEX WITH GTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-38; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: MELANOMA ANTIGEN NY-MEL-1; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RAB38; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RAB SMALL GTPASE, MEMBRANE TRAFFICKING, CELLULAR DYNAMICS, SIGNALING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.MCGRATH,D.WASCHBUSCH,A.R.KHAN REVDAT 3 17-JAN-24 6HDU 1 JRNL LINK REVDAT 2 27-NOV-19 6HDU 1 JRNL REVDAT 1 28-AUG-19 6HDU 0 JRNL AUTH E.MCGRATH,D.WASCHBUSCH,B.M.BAKER,A.R.KHAN JRNL TITL LRRK2 BINDS TO THE RAB32 SUBFAMILY IN A GTP-DEPENDENT JRNL TITL 2 MANNERVIAITS ARMADILLO DOMAIN. JRNL REF SMALL GTPASES 1 2019 JRNL REFN ESSN 2154-1256 JRNL PMID 31552791 JRNL DOI 10.1080/21541248.2019.1666623 REMARK 2 REMARK 2 RESOLUTION. 1.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.840 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 66457 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 3358 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 49.2987 - 5.1687 0.98 2695 140 0.2084 0.2221 REMARK 3 2 5.1687 - 4.1032 1.00 2663 160 0.1585 0.1764 REMARK 3 3 4.1032 - 3.5847 1.00 2645 158 0.1641 0.1832 REMARK 3 4 3.5847 - 3.2570 1.00 2656 143 0.1683 0.1872 REMARK 3 5 3.2570 - 3.0236 1.00 2648 139 0.1790 0.1926 REMARK 3 6 3.0236 - 2.8454 1.00 2668 132 0.1870 0.2038 REMARK 3 7 2.8454 - 2.7029 1.00 2630 167 0.1901 0.1982 REMARK 3 8 2.7029 - 2.5852 1.00 2657 139 0.1883 0.2211 REMARK 3 9 2.5852 - 2.4857 1.00 2654 129 0.1929 0.2159 REMARK 3 10 2.4857 - 2.3999 1.00 2630 147 0.1902 0.2294 REMARK 3 11 2.3999 - 2.3249 1.00 2623 139 0.1865 0.2152 REMARK 3 12 2.3249 - 2.2584 1.00 2637 139 0.1835 0.2217 REMARK 3 13 2.2584 - 2.1990 1.00 2635 155 0.1785 0.2156 REMARK 3 14 2.1990 - 2.1453 1.00 2636 144 0.1883 0.2366 REMARK 3 15 2.1453 - 2.0966 1.00 2631 145 0.1856 0.2204 REMARK 3 16 2.0966 - 2.0519 0.99 2631 136 0.1873 0.2493 REMARK 3 17 2.0519 - 2.0109 1.00 2589 159 0.2019 0.2393 REMARK 3 18 2.0109 - 1.9730 0.99 2659 148 0.2218 0.2636 REMARK 3 19 1.9730 - 1.9377 1.00 2629 125 0.2203 0.2411 REMARK 3 20 1.9377 - 1.9049 1.00 2649 127 0.2279 0.2465 REMARK 3 21 1.9049 - 1.8741 1.00 2616 154 0.2296 0.2672 REMARK 3 22 1.8741 - 1.8453 1.00 2656 121 0.2502 0.3167 REMARK 3 23 1.8453 - 1.8182 1.00 2629 121 0.2552 0.2796 REMARK 3 24 1.8182 - 1.7926 0.86 2333 91 0.2728 0.2706 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) : 25.880 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 : 0.005 5867 REMARK 3 ANGLE : 0.796 7978 REMARK 3 CHIRALITY : 0.054 867 REMARK 3 PLANARITY : 0.005 988 REMARK 3 DIHEDRAL : 10.491 4433 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 6HDU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1200011537. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JAN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 66651 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 REMARK 200 RESOLUTION RANGE LOW (A) : 49.280 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.65200 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: 6FF8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MORPHEUS A9 10% PEG 20000 20% PEG 550 REMARK 280 MME 0.02M DIVALENT CATIONS 0.1M BICINE/TRIZMA BASE PH 8.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 288K 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 35.49650 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 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: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 GLY A 132 REMARK 465 LYS A 133 REMARK 465 ASP A 134 REMARK 465 VAL A 135 REMARK 465 LEU A 136 REMARK 465 MET A 137 REMARK 465 ASN A 138 REMARK 465 ASN A 139 REMARK 465 GLY A 140 REMARK 465 LEU A 141 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 GLY B 132 REMARK 465 LYS B 133 REMARK 465 ASP B 134 REMARK 465 VAL B 135 REMARK 465 LEU B 136 REMARK 465 MET B 137 REMARK 465 ASN B 138 REMARK 465 ASN B 139 REMARK 465 GLY B 140 REMARK 465 LEU B 141 REMARK 465 LYS B 142 REMARK 465 GLU B 181 REMARK 465 GLY C -2 REMARK 465 SER C -1 REMARK 465 HIS C 0 REMARK 465 GLY C 132 REMARK 465 LYS C 133 REMARK 465 ASP C 134 REMARK 465 VAL C 135 REMARK 465 LEU C 136 REMARK 465 MET C 137 REMARK 465 ASN C 138 REMARK 465 ASN C 139 REMARK 465 GLY C 140 REMARK 465 LEU C 141 REMARK 465 GLU C 181 REMARK 465 GLY D -2 REMARK 465 GLY D 132 REMARK 465 LYS D 133 REMARK 465 ASP D 134 REMARK 465 VAL D 135 REMARK 465 LEU D 136 REMARK 465 MET D 137 REMARK 465 ASN D 138 REMARK 465 ASN D 139 REMARK 465 GLY D 140 REMARK 465 LEU D 141 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 C 1009 O HOH C 1138 1.89 REMARK 500 O HOH D 1003 O HOH D 1114 1.91 REMARK 500 O HOH B 1148 O HOH B 1156 1.92 REMARK 500 ND2 ASN A 116 O HOH A 1001 1.93 REMARK 500 OD1 ASN C 33 O HOH C 1001 1.97 REMARK 500 O HOH D 1007 O HOH D 1177 1.97 REMARK 500 O HOH B 1089 O HOH B 1094 1.98 REMARK 500 OD1 ASN D 106 O HOH D 1001 1.99 REMARK 500 NH1 ARG B 81 O HOH B 1001 2.01 REMARK 500 O HOH D 1142 O HOH D 1145 2.01 REMARK 500 O HOH A 1090 O HOH A 1130 2.02 REMARK 500 O HOH B 1155 O HOH B 1158 2.02 REMARK 500 N HIS A 0 O HOH A 1002 2.03 REMARK 500 O HOH C 1142 O HOH C 1157 2.05 REMARK 500 O HOH B 1018 O HOH B 1115 2.06 REMARK 500 N SER D -1 O HOH D 1002 2.06 REMARK 500 O HOH A 1154 O HOH B 1138 2.11 REMARK 500 O HOH D 1111 O HOH D 1159 2.11 REMARK 500 OE1 GLU C 157 O HOH C 1002 2.12 REMARK 500 NE2 GLN C 62 O HOH C 1003 2.14 REMARK 500 OE2 GLU D 168 O HOH D 1003 2.16 REMARK 500 O HOH A 1062 O HOH A 1142 2.17 REMARK 500 NH2 ARG B 39 O HOH B 1002 2.17 REMARK 500 O HOH D 1156 O HOH D 1183 2.18 REMARK 500 OD1 ASN A 106 O HOH A 1003 2.18 REMARK 500 O HOH B 1026 O HOH B 1143 2.18 REMARK 500 O HOH C 1002 O HOH C 1150 2.18 REMARK 500 SG CYS D 172 O HOH D 1163 2.19 REMARK 500 O HOH B 1036 O HOH B 1144 2.19 REMARK 500 O HOH C 1151 O HOH C 1188 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 C 1175 O HOH D 1198 1556 1.97 REMARK 500 O HOH A 1073 O HOH B 1063 1565 2.09 REMARK 500 O HOH A 1006 O HOH C 1063 2657 2.18 REMARK 500 O HOH B 1097 O HOH D 1169 2747 2.19 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 ASP B 144 -55.32 -134.88 REMARK 500 PRO C 55 -19.54 -48.75 REMARK 500 LYS C 128 32.41 72.96 REMARK 500 PRO D 55 -9.06 -55.37 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 B1158 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH D1198 DISTANCE = 6.06 ANGSTROMS REMARK 525 HOH D1199 DISTANCE = 6.09 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 A 901 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 23 OG1 REMARK 620 2 THR A 41 OG1 83.8 REMARK 620 3 GTP A 900 O3G 176.7 93.1 REMARK 620 4 GTP A 900 O2B 89.9 173.4 93.1 REMARK 620 5 HOH A1010 O 85.5 90.3 93.3 91.3 REMARK 620 6 HOH A1020 O 88.7 93.5 92.8 84.3 172.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 901 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 23 OG1 REMARK 620 2 THR B 41 OG1 84.3 REMARK 620 3 GTP B 900 O3G 173.5 91.4 REMARK 620 4 GTP B 900 O2B 90.8 174.7 93.4 REMARK 620 5 HOH B1027 O 89.2 85.8 85.6 92.3 REMARK 620 6 HOH B1030 O 93.6 95.1 91.6 87.1 177.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 901 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR C 23 OG1 REMARK 620 2 THR C 41 OG1 84.1 REMARK 620 3 GTP C 900 O1G 174.9 90.8 REMARK 620 4 GTP C 900 O1B 93.0 175.9 92.1 REMARK 620 5 HOH C1021 O 88.6 88.9 90.9 93.9 REMARK 620 6 HOH C1035 O 91.0 90.5 89.5 86.7 179.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D 901 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR D 23 OG1 REMARK 620 2 THR D 41 OG1 83.6 REMARK 620 3 GTP D 900 O3G 175.3 92.6 REMARK 620 4 GTP D 900 O2B 92.7 173.4 91.3 REMARK 620 5 HOH D1015 O 86.0 90.5 91.3 94.7 REMARK 620 6 HOH D1028 O 91.0 90.3 91.7 84.2 176.8 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 GTP A 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GTP B 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GTP C 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG C 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GTP D 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG D 901 DBREF 6HDU A 1 181 UNP P57729 RAB38_HUMAN 1 181 DBREF 6HDU B 1 181 UNP P57729 RAB38_HUMAN 1 181 DBREF 6HDU C 1 181 UNP P57729 RAB38_HUMAN 1 181 DBREF 6HDU D 1 181 UNP P57729 RAB38_HUMAN 1 181 SEQADV 6HDU GLY A -2 UNP P57729 EXPRESSION TAG SEQADV 6HDU SER A -1 UNP P57729 EXPRESSION TAG SEQADV 6HDU HIS A 0 UNP P57729 EXPRESSION TAG SEQADV 6HDU LEU A 69 UNP P57729 GLN 69 ENGINEERED MUTATION SEQADV 6HDU GLY B -2 UNP P57729 EXPRESSION TAG SEQADV 6HDU SER B -1 UNP P57729 EXPRESSION TAG SEQADV 6HDU HIS B 0 UNP P57729 EXPRESSION TAG SEQADV 6HDU LEU B 69 UNP P57729 GLN 69 ENGINEERED MUTATION SEQADV 6HDU GLY C -2 UNP P57729 EXPRESSION TAG SEQADV 6HDU SER C -1 UNP P57729 EXPRESSION TAG SEQADV 6HDU HIS C 0 UNP P57729 EXPRESSION TAG SEQADV 6HDU LEU C 69 UNP P57729 GLN 69 ENGINEERED MUTATION SEQADV 6HDU GLY D -2 UNP P57729 EXPRESSION TAG SEQADV 6HDU SER D -1 UNP P57729 EXPRESSION TAG SEQADV 6HDU HIS D 0 UNP P57729 EXPRESSION TAG SEQADV 6HDU LEU D 69 UNP P57729 GLN 69 ENGINEERED MUTATION SEQRES 1 A 184 GLY SER HIS MET GLN ALA PRO HIS LYS GLU HIS LEU TYR SEQRES 2 A 184 LYS LEU LEU VAL ILE GLY ASP LEU GLY VAL GLY LYS THR SEQRES 3 A 184 SER ILE ILE LYS ARG TYR VAL HIS GLN ASN PHE SER SER SEQRES 4 A 184 HIS TYR ARG ALA THR ILE GLY VAL ASP PHE ALA LEU LYS SEQRES 5 A 184 VAL LEU HIS TRP ASP PRO GLU THR VAL VAL ARG LEU GLN SEQRES 6 A 184 LEU TRP ASP ILE ALA GLY LEU GLU ARG PHE GLY ASN MET SEQRES 7 A 184 THR ARG VAL TYR TYR ARG GLU ALA MET GLY ALA PHE ILE SEQRES 8 A 184 VAL PHE ASP VAL THR ARG PRO ALA THR PHE GLU ALA VAL SEQRES 9 A 184 ALA LYS TRP LYS ASN ASP LEU ASP SER LYS LEU SER LEU SEQRES 10 A 184 PRO ASN GLY LYS PRO VAL SER VAL VAL LEU LEU ALA ASN SEQRES 11 A 184 LYS CYS ASP GLN GLY LYS ASP VAL LEU MET ASN ASN GLY SEQRES 12 A 184 LEU LYS MET ASP GLN PHE CYS LYS GLU HIS GLY PHE VAL SEQRES 13 A 184 GLY TRP PHE GLU THR SER ALA LYS GLU ASN ILE ASN ILE SEQRES 14 A 184 ASP GLU ALA SER ARG CYS LEU VAL LYS HIS ILE LEU ALA SEQRES 15 A 184 ASN GLU SEQRES 1 B 184 GLY SER HIS MET GLN ALA PRO HIS LYS GLU HIS LEU TYR SEQRES 2 B 184 LYS LEU LEU VAL ILE GLY ASP LEU GLY VAL GLY LYS THR SEQRES 3 B 184 SER ILE ILE LYS ARG TYR VAL HIS GLN ASN PHE SER SER SEQRES 4 B 184 HIS TYR ARG ALA THR ILE GLY VAL ASP PHE ALA LEU LYS SEQRES 5 B 184 VAL LEU HIS TRP ASP PRO GLU THR VAL VAL ARG LEU GLN SEQRES 6 B 184 LEU TRP ASP ILE ALA GLY LEU GLU ARG PHE GLY ASN MET SEQRES 7 B 184 THR ARG VAL TYR TYR ARG GLU ALA MET GLY ALA PHE ILE SEQRES 8 B 184 VAL PHE ASP VAL THR ARG PRO ALA THR PHE GLU ALA VAL SEQRES 9 B 184 ALA LYS TRP LYS ASN ASP LEU ASP SER LYS LEU SER LEU SEQRES 10 B 184 PRO ASN GLY LYS PRO VAL SER VAL VAL LEU LEU ALA ASN SEQRES 11 B 184 LYS CYS ASP GLN GLY LYS ASP VAL LEU MET ASN ASN GLY SEQRES 12 B 184 LEU LYS MET ASP GLN PHE CYS LYS GLU HIS GLY PHE VAL SEQRES 13 B 184 GLY TRP PHE GLU THR SER ALA LYS GLU ASN ILE ASN ILE SEQRES 14 B 184 ASP GLU ALA SER ARG CYS LEU VAL LYS HIS ILE LEU ALA SEQRES 15 B 184 ASN GLU SEQRES 1 C 184 GLY SER HIS MET GLN ALA PRO HIS LYS GLU HIS LEU TYR SEQRES 2 C 184 LYS LEU LEU VAL ILE GLY ASP LEU GLY VAL GLY LYS THR SEQRES 3 C 184 SER ILE ILE LYS ARG TYR VAL HIS GLN ASN PHE SER SER SEQRES 4 C 184 HIS TYR ARG ALA THR ILE GLY VAL ASP PHE ALA LEU LYS SEQRES 5 C 184 VAL LEU HIS TRP ASP PRO GLU THR VAL VAL ARG LEU GLN SEQRES 6 C 184 LEU TRP ASP ILE ALA GLY LEU GLU ARG PHE GLY ASN MET SEQRES 7 C 184 THR ARG VAL TYR TYR ARG GLU ALA MET GLY ALA PHE ILE SEQRES 8 C 184 VAL PHE ASP VAL THR ARG PRO ALA THR PHE GLU ALA VAL SEQRES 9 C 184 ALA LYS TRP LYS ASN ASP LEU ASP SER LYS LEU SER LEU SEQRES 10 C 184 PRO ASN GLY LYS PRO VAL SER VAL VAL LEU LEU ALA ASN SEQRES 11 C 184 LYS CYS ASP GLN GLY LYS ASP VAL LEU MET ASN ASN GLY SEQRES 12 C 184 LEU LYS MET ASP GLN PHE CYS LYS GLU HIS GLY PHE VAL SEQRES 13 C 184 GLY TRP PHE GLU THR SER ALA LYS GLU ASN ILE ASN ILE SEQRES 14 C 184 ASP GLU ALA SER ARG CYS LEU VAL LYS HIS ILE LEU ALA SEQRES 15 C 184 ASN GLU SEQRES 1 D 184 GLY SER HIS MET GLN ALA PRO HIS LYS GLU HIS LEU TYR SEQRES 2 D 184 LYS LEU LEU VAL ILE GLY ASP LEU GLY VAL GLY LYS THR SEQRES 3 D 184 SER ILE ILE LYS ARG TYR VAL HIS GLN ASN PHE SER SER SEQRES 4 D 184 HIS TYR ARG ALA THR ILE GLY VAL ASP PHE ALA LEU LYS SEQRES 5 D 184 VAL LEU HIS TRP ASP PRO GLU THR VAL VAL ARG LEU GLN SEQRES 6 D 184 LEU TRP ASP ILE ALA GLY LEU GLU ARG PHE GLY ASN MET SEQRES 7 D 184 THR ARG VAL TYR TYR ARG GLU ALA MET GLY ALA PHE ILE SEQRES 8 D 184 VAL PHE ASP VAL THR ARG PRO ALA THR PHE GLU ALA VAL SEQRES 9 D 184 ALA LYS TRP LYS ASN ASP LEU ASP SER LYS LEU SER LEU SEQRES 10 D 184 PRO ASN GLY LYS PRO VAL SER VAL VAL LEU LEU ALA ASN SEQRES 11 D 184 LYS CYS ASP GLN GLY LYS ASP VAL LEU MET ASN ASN GLY SEQRES 12 D 184 LEU LYS MET ASP GLN PHE CYS LYS GLU HIS GLY PHE VAL SEQRES 13 D 184 GLY TRP PHE GLU THR SER ALA LYS GLU ASN ILE ASN ILE SEQRES 14 D 184 ASP GLU ALA SER ARG CYS LEU VAL LYS HIS ILE LEU ALA SEQRES 15 D 184 ASN GLU HET GTP A 900 32 HET MG A 901 1 HET GTP B 900 32 HET MG B 901 1 HET GTP C 900 32 HET MG C 901 1 HET GTP D 900 32 HET MG D 901 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 5 GTP 4(C10 H16 N5 O14 P3) FORMUL 6 MG 4(MG 2+) FORMUL 13 HOH *700(H2 O) HELIX 1 AA1 GLY A 21 GLN A 32 1 12 HELIX 2 AA2 GLY A 68 GLY A 73 5 6 HELIX 3 AA3 MET A 75 ARG A 81 1 7 HELIX 4 AA4 ARG A 94 LEU A 112 1 19 HELIX 5 AA5 MET A 143 GLY A 151 1 9 HELIX 6 AA6 ASN A 165 ASN A 180 1 16 HELIX 7 AA7 GLY B 21 GLN B 32 1 12 HELIX 8 AA8 GLY B 68 GLY B 73 5 6 HELIX 9 AA9 MET B 75 TYR B 80 1 6 HELIX 10 AB1 ARG B 94 LEU B 112 1 19 HELIX 11 AB2 ASP B 144 HIS B 150 1 7 HELIX 12 AB3 ASN B 165 ASN B 180 1 16 HELIX 13 AB4 GLY C 21 GLN C 32 1 12 HELIX 14 AB5 GLY C 68 GLY C 73 5 6 HELIX 15 AB6 MET C 75 ARG C 81 1 7 HELIX 16 AB7 ARG C 94 LEU C 112 1 19 HELIX 17 AB8 MET C 143 HIS C 150 1 8 HELIX 18 AB9 ASN C 165 ASN C 180 1 16 HELIX 19 AC1 SER D -1 ALA D 3 5 5 HELIX 20 AC2 GLY D 21 GLN D 32 1 12 HELIX 21 AC3 GLY D 68 GLY D 73 5 6 HELIX 22 AC4 MET D 75 ARG D 81 1 7 HELIX 23 AC5 ARG D 94 LEU D 112 1 19 HELIX 24 AC6 MET D 143 GLY D 151 1 9 HELIX 25 AC7 ASN D 165 ASN D 180 1 16 SHEET 1 AA1 6 VAL A 44 ASP A 54 0 SHEET 2 AA1 6 THR A 57 ILE A 66 -1 O LEU A 61 N LYS A 49 SHEET 3 AA1 6 LYS A 6 GLY A 16 1 N LEU A 12 O TRP A 64 SHEET 4 AA1 6 GLY A 85 ASP A 91 1 O PHE A 87 N LEU A 13 SHEET 5 AA1 6 SER A 121 ASN A 127 1 O LEU A 125 N ILE A 88 SHEET 6 AA1 6 GLY A 154 GLU A 157 1 O PHE A 156 N ALA A 126 SHEET 1 AA2 6 VAL B 44 ASP B 54 0 SHEET 2 AA2 6 THR B 57 ILE B 66 -1 O LEU B 63 N ALA B 47 SHEET 3 AA2 6 LYS B 6 ILE B 15 1 N HIS B 8 O ARG B 60 SHEET 4 AA2 6 GLY B 85 ASP B 91 1 O PHE B 87 N LEU B 13 SHEET 5 AA2 6 SER B 121 ASN B 127 1 O LEU B 125 N ILE B 88 SHEET 6 AA2 6 GLY B 154 GLU B 157 1 O PHE B 156 N ALA B 126 SHEET 1 AA3 6 VAL C 44 ASP C 54 0 SHEET 2 AA3 6 THR C 57 ILE C 66 -1 O ASP C 65 N ASP C 45 SHEET 3 AA3 6 LYS C 6 ILE C 15 1 N HIS C 8 O ARG C 60 SHEET 4 AA3 6 GLY C 85 ASP C 91 1 O PHE C 87 N LEU C 13 SHEET 5 AA3 6 SER C 121 ASN C 127 1 O LEU C 125 N ILE C 88 SHEET 6 AA3 6 GLY C 154 THR C 158 1 O PHE C 156 N ALA C 126 SHEET 1 AA4 6 VAL D 44 ASP D 54 0 SHEET 2 AA4 6 THR D 57 ILE D 66 -1 O ASP D 65 N ASP D 45 SHEET 3 AA4 6 LYS D 6 ILE D 15 1 N HIS D 8 O ARG D 60 SHEET 4 AA4 6 GLY D 85 ASP D 91 1 O PHE D 87 N LEU D 13 SHEET 5 AA4 6 SER D 121 ASN D 127 1 O LEU D 125 N ILE D 88 SHEET 6 AA4 6 GLY D 154 GLU D 157 1 O PHE D 156 N ALA D 126 LINK OG1 THR A 23 MG MG A 901 1555 1555 2.10 LINK OG1 THR A 41 MG MG A 901 1555 1555 2.10 LINK O3G GTP A 900 MG MG A 901 1555 1555 1.96 LINK O2B GTP A 900 MG MG A 901 1555 1555 2.10 LINK MG MG A 901 O HOH A1010 1555 1555 2.07 LINK MG MG A 901 O HOH A1020 1555 1555 2.15 LINK OG1 THR B 23 MG MG B 901 1555 1555 2.06 LINK OG1 THR B 41 MG MG B 901 1555 1555 2.10 LINK O3G GTP B 900 MG MG B 901 1555 1555 1.97 LINK O2B GTP B 900 MG MG B 901 1555 1555 2.05 LINK MG MG B 901 O HOH B1027 1555 1555 2.05 LINK MG MG B 901 O HOH B1030 1555 1555 2.08 LINK OG1 THR C 23 MG MG C 901 1555 1555 2.01 LINK OG1 THR C 41 MG MG C 901 1555 1555 2.14 LINK O1G GTP C 900 MG MG C 901 1555 1555 1.99 LINK O1B GTP C 900 MG MG C 901 1555 1555 2.01 LINK MG MG C 901 O HOH C1021 1555 1555 2.00 LINK MG MG C 901 O HOH C1035 1555 1555 2.12 LINK OG1 THR D 23 MG MG D 901 1555 1555 2.07 LINK OG1 THR D 41 MG MG D 901 1555 1555 2.10 LINK O3G GTP D 900 MG MG D 901 1555 1555 1.96 LINK O2B GTP D 900 MG MG D 901 1555 1555 2.05 LINK MG MG D 901 O HOH D1015 1555 1555 2.14 LINK MG MG D 901 O HOH D1028 1555 1555 2.16 SITE 1 AC1 26 LEU A 18 GLY A 19 VAL A 20 GLY A 21 SITE 2 AC1 26 LYS A 22 THR A 23 SER A 24 PHE A 34 SITE 3 AC1 26 SER A 35 SER A 36 TYR A 38 ALA A 40 SITE 4 AC1 26 THR A 41 GLY A 68 ASN A 127 LYS A 128 SITE 5 AC1 26 ASP A 130 GLN A 131 SER A 159 ALA A 160 SITE 6 AC1 26 LYS A 161 MG A 901 HOH A1010 HOH A1020 SITE 7 AC1 26 HOH A1037 HOH A1074 SITE 1 AC2 5 THR A 23 THR A 41 GTP A 900 HOH A1010 SITE 2 AC2 5 HOH A1020 SITE 1 AC3 26 LEU B 18 GLY B 19 VAL B 20 GLY B 21 SITE 2 AC3 26 LYS B 22 THR B 23 SER B 24 PHE B 34 SITE 3 AC3 26 SER B 35 SER B 36 TYR B 38 ALA B 40 SITE 4 AC3 26 THR B 41 GLY B 68 ASN B 127 LYS B 128 SITE 5 AC3 26 ASP B 130 GLN B 131 SER B 159 ALA B 160 SITE 6 AC3 26 LYS B 161 MG B 901 HOH B1027 HOH B1030 SITE 7 AC3 26 HOH B1039 HOH B1071 SITE 1 AC4 5 THR B 23 THR B 41 GTP B 900 HOH B1027 SITE 2 AC4 5 HOH B1030 SITE 1 AC5 26 LEU C 18 GLY C 19 VAL C 20 GLY C 21 SITE 2 AC5 26 LYS C 22 THR C 23 SER C 24 PHE C 34 SITE 3 AC5 26 SER C 35 SER C 36 TYR C 38 THR C 41 SITE 4 AC5 26 GLY C 68 ASN C 127 LYS C 128 ASP C 130 SITE 5 AC5 26 GLN C 131 SER C 159 ALA C 160 LYS C 161 SITE 6 AC5 26 MG C 901 HOH C1021 HOH C1035 HOH C1056 SITE 7 AC5 26 HOH C1057 HOH C1086 SITE 1 AC6 5 THR C 23 THR C 41 GTP C 900 HOH C1021 SITE 2 AC6 5 HOH C1035 SITE 1 AC7 25 LEU D 18 GLY D 19 VAL D 20 GLY D 21 SITE 2 AC7 25 LYS D 22 THR D 23 SER D 24 PHE D 34 SITE 3 AC7 25 SER D 35 SER D 36 TYR D 38 THR D 41 SITE 4 AC7 25 GLY D 68 ASN D 127 LYS D 128 ASP D 130 SITE 5 AC7 25 SER D 159 ALA D 160 LYS D 161 MG D 901 SITE 6 AC7 25 HOH D1015 HOH D1028 HOH D1039 HOH D1044 SITE 7 AC7 25 HOH D1110 SITE 1 AC8 5 THR D 23 THR D 41 GTP D 900 HOH D1015 SITE 2 AC8 5 HOH D1028 CRYST1 70.045 70.993 74.487 90.00 102.21 90.00 P 1 21 1 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 0.014277 0.000000 0.003089 0.00000 SCALE2 0.000000 0.014086 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013736 0.00000