HEADER ENDOCYTOSIS 31-MAY-24 8ZQ3 TITLE STRUCTURE OF ORP1L-RAB7A IN THE PRESENCE OF GDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-7A; COMPND 3 CHAIN: A; COMPND 4 EC: 3.6.5.2; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: OXYSTEROL-BINDING PROTEIN-RELATED PROTEIN 1; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: ORP-1,OSBP-RELATED PROTEIN 1; COMPND 11 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: RAB7A, RAB7; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: OSBPL1A, ORP1, OSBP8, OSBPL1, OSBPL1B; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXYSTEROL BINDING PROTEIN (OSBP) THE HUMAN OSBP-RELATED GENE/PROTEIN KEYWDS 2 (ORP) FAMILY, ENDOCYTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR Q.LU,J.ZHANG,C.XU REVDAT 1 26-JUN-24 8ZQ3 0 JRNL AUTH Q.LU,Z.ZHU,J.ZHANG,C.XU JRNL TITL STRUCTURE OF GDP-BOUND RAB7 Q67L IN COMPLEX WITH ORP1L. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 725 50232 2024 JRNL REFN ESSN 1090-2104 JRNL PMID 38897042 JRNL DOI 10.1016/J.BBRC.2024.150232 REMARK 2 REMARK 2 RESOLUTION. 2.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 17217 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1722 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 40.2100 - 5.5592 1.00 1436 160 0.1759 0.2044 REMARK 3 2 5.5592 - 4.4143 1.00 1322 146 0.1688 0.1994 REMARK 3 3 4.4143 - 3.8568 1.00 1311 147 0.1636 0.1951 REMARK 3 4 3.8568 - 3.5044 1.00 1279 141 0.1874 0.2197 REMARK 3 5 3.5044 - 3.2533 1.00 1288 144 0.2128 0.2313 REMARK 3 6 3.2533 - 3.0616 1.00 1278 141 0.2459 0.2744 REMARK 3 7 3.0616 - 2.9083 1.00 1268 141 0.2290 0.2959 REMARK 3 8 2.9083 - 2.7817 1.00 1271 142 0.2396 0.2868 REMARK 3 9 2.7817 - 2.6747 1.00 1276 141 0.2476 0.3082 REMARK 3 10 2.6747 - 2.5824 1.00 1244 138 0.2561 0.3133 REMARK 3 11 2.5824 - 2.5017 1.00 1271 142 0.2708 0.3698 REMARK 3 12 2.5017 - 2.4302 1.00 1251 139 0.2821 0.3525 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.540 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 : 0.008 2583 REMARK 3 ANGLE : 1.016 3512 REMARK 3 CHIRALITY : 0.055 411 REMARK 3 PLANARITY : 0.006 453 REMARK 3 DIHEDRAL : 9.737 1549 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 13 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 7 THROUGH 30 ) REMARK 3 ORIGIN FOR THE GROUP (A): -28.1937 -2.6786 -9.2705 REMARK 3 T TENSOR REMARK 3 T11: 0.3868 T22: 0.7932 REMARK 3 T33: 0.6137 T12: 0.0741 REMARK 3 T13: -0.0021 T23: -0.0054 REMARK 3 L TENSOR REMARK 3 L11: 3.1518 L22: 2.5796 REMARK 3 L33: 3.9366 L12: -0.3171 REMARK 3 L13: 1.1202 L23: 0.3172 REMARK 3 S TENSOR REMARK 3 S11: 0.4934 S12: -0.7162 S13: -0.7620 REMARK 3 S21: -0.0385 S22: -0.2759 S23: -0.2687 REMARK 3 S31: 0.6587 S32: 0.3302 S33: -0.2008 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 31 THROUGH 40 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.5481 -7.9631 -3.3022 REMARK 3 T TENSOR REMARK 3 T11: 0.7885 T22: 1.2227 REMARK 3 T33: 1.0294 T12: 0.2317 REMARK 3 T13: -0.0631 T23: 0.1071 REMARK 3 L TENSOR REMARK 3 L11: 1.9789 L22: 0.1987 REMARK 3 L33: 9.7460 L12: -0.6000 REMARK 3 L13: -3.0707 L23: 1.1375 REMARK 3 S TENSOR REMARK 3 S11: -0.7120 S12: -0.7643 S13: -0.7125 REMARK 3 S21: 0.1959 S22: 0.8795 S23: 0.5691 REMARK 3 S31: 2.0335 S32: 1.3081 S33: -0.1906 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 41 THROUGH 55 ) REMARK 3 ORIGIN FOR THE GROUP (A): -28.4368 6.8308 -5.1064 REMARK 3 T TENSOR REMARK 3 T11: 0.5877 T22: 1.1773 REMARK 3 T33: 1.0170 T12: -0.2976 REMARK 3 T13: -0.2029 T23: -0.2271 REMARK 3 L TENSOR REMARK 3 L11: 2.9340 L22: 8.3642 REMARK 3 L33: 3.2343 L12: 0.3424 REMARK 3 L13: -2.3242 L23: 0.7608 REMARK 3 S TENSOR REMARK 3 S11: 0.4842 S12: -1.5314 S13: 1.1181 REMARK 3 S21: -0.9196 S22: 0.1127 S23: 1.4776 REMARK 3 S31: -0.4383 S32: -0.6620 S33: -0.4381 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 56 THROUGH 110 ) REMARK 3 ORIGIN FOR THE GROUP (A): -36.4816 -6.0571 -12.7018 REMARK 3 T TENSOR REMARK 3 T11: 0.5774 T22: 0.6771 REMARK 3 T33: 0.6267 T12: -0.0200 REMARK 3 T13: -0.0266 T23: 0.0783 REMARK 3 L TENSOR REMARK 3 L11: 5.7215 L22: 2.8363 REMARK 3 L33: 2.9901 L12: 1.5100 REMARK 3 L13: 0.7078 L23: 1.2829 REMARK 3 S TENSOR REMARK 3 S11: 0.2594 S12: -0.4411 S13: -0.5440 REMARK 3 S21: -0.0110 S22: -0.1688 S23: -0.0621 REMARK 3 S31: 0.2288 S32: -0.1237 S33: 0.0016 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 111 THROUGH 125 ) REMARK 3 ORIGIN FOR THE GROUP (A): -39.9373 1.3512 -18.0558 REMARK 3 T TENSOR REMARK 3 T11: 0.3849 T22: 0.6840 REMARK 3 T33: 0.6261 T12: -0.0596 REMARK 3 T13: -0.0338 T23: 0.0038 REMARK 3 L TENSOR REMARK 3 L11: 9.9087 L22: 3.5712 REMARK 3 L33: 2.7415 L12: -2.6897 REMARK 3 L13: -2.4690 L23: 0.0261 REMARK 3 S TENSOR REMARK 3 S11: 0.0883 S12: 1.6561 S13: 1.3953 REMARK 3 S21: -0.1827 S22: -0.3046 S23: -0.0962 REMARK 3 S31: 0.1501 S32: -0.1200 S33: 0.1503 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 126 THROUGH 161 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.2336 -4.8180 -24.9169 REMARK 3 T TENSOR REMARK 3 T11: 0.6452 T22: 0.9697 REMARK 3 T33: 0.5153 T12: -0.0912 REMARK 3 T13: 0.0386 T23: -0.1261 REMARK 3 L TENSOR REMARK 3 L11: 4.2860 L22: 2.3141 REMARK 3 L33: 6.3143 L12: 0.7839 REMARK 3 L13: 1.6818 L23: -0.9044 REMARK 3 S TENSOR REMARK 3 S11: -0.3258 S12: 1.1898 S13: 0.0889 REMARK 3 S21: -0.5596 S22: 0.2451 S23: -0.3679 REMARK 3 S31: 0.5096 S32: 0.4411 S33: 0.0598 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 162 THROUGH 180 ) REMARK 3 ORIGIN FOR THE GROUP (A): -32.1609 8.8505 -14.5939 REMARK 3 T TENSOR REMARK 3 T11: 0.6877 T22: 0.8167 REMARK 3 T33: 1.1475 T12: -0.0834 REMARK 3 T13: 0.1981 T23: -0.0748 REMARK 3 L TENSOR REMARK 3 L11: 5.7329 L22: 7.8948 REMARK 3 L33: 8.2387 L12: 1.6480 REMARK 3 L13: 0.9994 L23: -1.4503 REMARK 3 S TENSOR REMARK 3 S11: 0.8677 S12: -0.1276 S13: 1.9420 REMARK 3 S21: 0.1585 S22: 0.1304 S23: 1.5657 REMARK 3 S31: -1.0856 S32: -0.3806 S33: -0.8943 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 29 ) REMARK 3 ORIGIN FOR THE GROUP (A): -54.7451 -13.8576 -29.7069 REMARK 3 T TENSOR REMARK 3 T11: 0.6346 T22: 0.6065 REMARK 3 T33: 0.6213 T12: 0.0778 REMARK 3 T13: -0.0528 T23: -0.0918 REMARK 3 L TENSOR REMARK 3 L11: 5.1589 L22: 4.2821 REMARK 3 L33: 4.0403 L12: 0.6634 REMARK 3 L13: 0.2292 L23: 0.3848 REMARK 3 S TENSOR REMARK 3 S11: 0.2592 S12: 0.7377 S13: -0.5211 REMARK 3 S21: -0.4850 S22: 0.0770 S23: -0.5058 REMARK 3 S31: 0.3499 S32: 0.3927 S33: -0.3591 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 30 THROUGH 43 ) REMARK 3 ORIGIN FOR THE GROUP (A): -59.3223 -19.0576 -24.5060 REMARK 3 T TENSOR REMARK 3 T11: 1.0444 T22: 0.6008 REMARK 3 T33: 0.7937 T12: -0.1548 REMARK 3 T13: -0.0464 T23: 0.1068 REMARK 3 L TENSOR REMARK 3 L11: 4.2832 L22: 2.6149 REMARK 3 L33: 3.6206 L12: -1.4411 REMARK 3 L13: -0.7801 L23: 0.2368 REMARK 3 S TENSOR REMARK 3 S11: 0.3462 S12: -0.5733 S13: -1.1949 REMARK 3 S21: -0.2331 S22: -0.2500 S23: 0.4488 REMARK 3 S31: 1.6050 S32: -0.1526 S33: -0.1310 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 44 THROUGH 93 ) REMARK 3 ORIGIN FOR THE GROUP (A): -58.1116 -4.9332 -19.2578 REMARK 3 T TENSOR REMARK 3 T11: 0.5123 T22: 0.5411 REMARK 3 T33: 0.4732 T12: -0.0403 REMARK 3 T13: 0.0013 T23: 0.0355 REMARK 3 L TENSOR REMARK 3 L11: 3.2936 L22: 3.5612 REMARK 3 L33: 2.0447 L12: -0.7500 REMARK 3 L13: -1.4052 L23: 1.5233 REMARK 3 S TENSOR REMARK 3 S11: -0.1227 S12: -0.3834 S13: -0.1960 REMARK 3 S21: -0.0182 S22: 0.1285 S23: -0.1300 REMARK 3 S31: 0.2071 S32: -0.2288 S33: -0.0095 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 94 THROUGH 102 ) REMARK 3 ORIGIN FOR THE GROUP (A): -65.2521 3.9808 -22.5067 REMARK 3 T TENSOR REMARK 3 T11: 0.3941 T22: 0.6630 REMARK 3 T33: 0.5846 T12: -0.0654 REMARK 3 T13: -0.0584 T23: 0.0293 REMARK 3 L TENSOR REMARK 3 L11: 3.1458 L22: 7.1768 REMARK 3 L33: 4.3992 L12: 2.9471 REMARK 3 L13: -2.6059 L23: -0.8812 REMARK 3 S TENSOR REMARK 3 S11: 0.0684 S12: 0.6165 S13: 0.1582 REMARK 3 S21: 0.1993 S22: 0.1854 S23: 0.1403 REMARK 3 S31: -0.5888 S32: -0.5428 S33: -0.2309 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 103 THROUGH 123 ) REMARK 3 ORIGIN FOR THE GROUP (A): -63.5094 1.5659 -9.8847 REMARK 3 T TENSOR REMARK 3 T11: 0.5301 T22: 0.6753 REMARK 3 T33: 0.4971 T12: 0.0441 REMARK 3 T13: -0.0178 T23: -0.0065 REMARK 3 L TENSOR REMARK 3 L11: 3.1507 L22: 4.6300 REMARK 3 L33: 4.2640 L12: -2.0399 REMARK 3 L13: -0.7942 L23: -2.6909 REMARK 3 S TENSOR REMARK 3 S11: 0.1647 S12: -0.7344 S13: -0.3504 REMARK 3 S21: 0.7852 S22: -0.0219 S23: 0.3477 REMARK 3 S31: -0.4307 S32: -0.2318 S33: -0.0819 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 124 THROUGH 148 ) REMARK 3 ORIGIN FOR THE GROUP (A): -74.0331 5.2203 -9.0546 REMARK 3 T TENSOR REMARK 3 T11: 0.5646 T22: 0.4419 REMARK 3 T33: 0.4204 T12: 0.0141 REMARK 3 T13: -0.0490 T23: 0.0320 REMARK 3 L TENSOR REMARK 3 L11: 8.6931 L22: 7.7813 REMARK 3 L33: 6.6462 L12: 5.4164 REMARK 3 L13: -4.6757 L23: -2.2750 REMARK 3 S TENSOR REMARK 3 S11: 1.1327 S12: -0.5598 S13: -0.0069 REMARK 3 S21: 1.4813 S22: -0.3996 S23: -0.0679 REMARK 3 S31: -0.6253 S32: 0.1059 S33: -0.7675 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 8ZQ3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 04-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1300048331. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : STFC LARGE PIXEL DETECTOR REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17217 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.430 REMARK 200 RESOLUTION RANGE LOW (A) : 44.720 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 25.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.50 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1T91 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M DIAMMONIUM TARTRATE, 20% PEG3350, REMARK 280 0.1 M ETHYLENEDIAMINETETRAACETIC ACID DISODIUM SALT DIHYDRATE, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 2 2 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 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+3/4 REMARK 290 8555 -Y,-X,-Z+1/4 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 67.08000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 33.54000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 100.62000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 67.08000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 100.62000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 33.54000 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 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 1 REMARK 465 THR A 2 REMARK 465 SER A 3 REMARK 465 ARG A 4 REMARK 465 LYS A 5 REMARK 465 GLU A 185 REMARK 465 PHE A 186 REMARK 465 PRO A 187 REMARK 465 GLU A 188 REMARK 465 PRO A 189 REMARK 465 ILE A 190 REMARK 465 LYS A 191 REMARK 465 LEU A 192 REMARK 465 ASP A 193 REMARK 465 LYS A 194 REMARK 465 ASN A 195 REMARK 465 ASP A 196 REMARK 465 ARG A 197 REMARK 465 ALA A 198 REMARK 465 LYS A 199 REMARK 465 ALA A 200 REMARK 465 SER A 201 REMARK 465 ALA A 202 REMARK 465 GLU A 203 REMARK 465 SER A 204 REMARK 465 CYS A 205 REMARK 465 SER A 206 REMARK 465 CYS A 207 REMARK 465 LYS B 153 REMARK 465 THR B 154 REMARK 465 THR B 155 REMARK 465 GLU B 156 REMARK 465 LEU B 157 REMARK 465 THR B 158 REMARK 465 ALA B 159 REMARK 465 LEU B 160 REMARK 465 LEU B 161 REMARK 465 ASN B 162 REMARK 465 ARG B 163 REMARK 465 PRO B 164 REMARK 465 ASN B 165 REMARK 465 PRO B 166 REMARK 465 PRO B 167 REMARK 465 ASP B 168 REMARK 465 VAL B 169 REMARK 465 ASN B 170 REMARK 465 CYS B 171 REMARK 465 SER B 172 REMARK 465 ASP B 173 REMARK 465 GLN B 174 REMARK 465 LEU B 175 REMARK 465 GLY B 176 REMARK 465 ASN B 177 REMARK 465 THR B 178 REMARK 465 PRO B 179 REMARK 465 LEU B 180 REMARK 465 HIS B 181 REMARK 465 CYS B 182 REMARK 465 ALA B 183 REMARK 465 ALA B 184 REMARK 465 TYR B 185 REMARK 465 ARG B 186 REMARK 465 ALA B 187 REMARK 465 HIS B 188 REMARK 465 LYS B 189 REMARK 465 GLN B 190 REMARK 465 CYS B 191 REMARK 465 ALA B 192 REMARK 465 LEU B 193 REMARK 465 LYS B 194 REMARK 465 LEU B 195 REMARK 465 LEU B 196 REMARK 465 ARG B 197 REMARK 465 SER B 198 REMARK 465 GLY B 199 REMARK 465 ALA B 200 REMARK 465 ASP B 201 REMARK 465 PRO B 202 REMARK 465 ASN B 203 REMARK 465 LEU B 204 REMARK 465 LYS B 205 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 LYS A 6 CD CE NZ REMARK 470 LYS A 32 CG CD CE NZ REMARK 470 LYS A 38 CG CD CE NZ REMARK 470 THR A 40 OG1 CG2 REMARK 470 ASP A 44 CG OD1 OD2 REMARK 470 ASP A 54 CG OD1 OD2 REMARK 470 GLU A 68 CD OE1 OE2 REMARK 470 ARG A 69 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 70 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN A 71 CG CD OE1 NE2 REMARK 470 SER A 72 OG REMARK 470 LEU A 73 CD1 CD2 REMARK 470 ARG A 79 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 94 CG OD1 ND2 REMARK 470 LYS A 97 CG CD CE NZ REMARK 470 GLU A 130 CD OE1 OE2 REMARK 470 ASN A 131 CG OD1 ND2 REMARK 470 LYS A 137 CE NZ REMARK 470 LYS A 157 CD CE NZ REMARK 470 GLU A 158 OE1 OE2 REMARK 470 LYS A 175 NZ REMARK 470 GLU A 179 CG CD OE1 OE2 REMARK 470 GLU A 181 CG CD OE1 OE2 REMARK 470 TYR A 183 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASN A 184 CG OD1 ND2 REMARK 470 MET B 1 CG SD CE REMARK 470 GLU B 4 OE1 OE2 REMARK 470 GLU B 32 CG CD OE1 OE2 REMARK 470 LYS B 44 CG CD CE NZ REMARK 470 LYS B 140 CE NZ REMARK 470 ARG B 150 NE CZ NH1 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 LYS A 38 12.74 -68.54 REMARK 500 PHE A 45 173.24 -59.50 REMARK 500 LEU A 46 137.29 -170.84 REMARK 500 SER A 145 -39.71 -36.48 REMARK 500 LYS A 146 50.34 -96.53 REMARK 500 ASN A 161 17.36 58.04 REMARK 500 GLU A 181 108.08 73.41 REMARK 500 ALA B 35 115.16 -166.61 REMARK 500 ASN B 46 21.75 -159.42 REMARK 500 REMARK 500 REMARK: NULL DBREF 8ZQ3 A 1 207 UNP P51149 RAB7A_HUMAN 1 207 DBREF 8ZQ3 B 1 205 UNP Q9BXW6 OSBL1_HUMAN 1 205 SEQADV 8ZQ3 LEU A 67 UNP P51149 GLN 67 ENGINEERED MUTATION SEQRES 1 A 207 MET THR SER ARG LYS LYS VAL LEU LEU LYS VAL ILE ILE SEQRES 2 A 207 LEU GLY ASP SER GLY VAL GLY LYS THR SER LEU MET ASN SEQRES 3 A 207 GLN TYR VAL ASN LYS LYS PHE SER ASN GLN TYR LYS ALA SEQRES 4 A 207 THR ILE GLY ALA ASP PHE LEU THR LYS GLU VAL MET VAL SEQRES 5 A 207 ASP ASP ARG LEU VAL THR MET GLN ILE TRP ASP THR ALA SEQRES 6 A 207 GLY LEU GLU ARG PHE GLN SER LEU GLY VAL ALA PHE TYR SEQRES 7 A 207 ARG GLY ALA ASP CYS CYS VAL LEU VAL PHE ASP VAL THR SEQRES 8 A 207 ALA PRO ASN THR PHE LYS THR LEU ASP SER TRP ARG ASP SEQRES 9 A 207 GLU PHE LEU ILE GLN ALA SER PRO ARG ASP PRO GLU ASN SEQRES 10 A 207 PHE PRO PHE VAL VAL LEU GLY ASN LYS ILE ASP LEU GLU SEQRES 11 A 207 ASN ARG GLN VAL ALA THR LYS ARG ALA GLN ALA TRP CYS SEQRES 12 A 207 TYR SER LYS ASN ASN ILE PRO TYR PHE GLU THR SER ALA SEQRES 13 A 207 LYS GLU ALA ILE ASN VAL GLU GLN ALA PHE GLN THR ILE SEQRES 14 A 207 ALA ARG ASN ALA LEU LYS GLN GLU THR GLU VAL GLU LEU SEQRES 15 A 207 TYR ASN GLU PHE PRO GLU PRO ILE LYS LEU ASP LYS ASN SEQRES 16 A 207 ASP ARG ALA LYS ALA SER ALA GLU SER CYS SER CYS SEQRES 1 B 205 MET ASN THR GLU ALA GLU GLN GLN LEU LEU HIS HIS ALA SEQRES 2 B 205 ARG ASN GLY ASN ALA GLU GLU VAL ARG GLN LEU LEU GLU SEQRES 3 B 205 THR MET ALA ARG ASN GLU VAL ILE ALA ASP ILE ASN CYS SEQRES 4 B 205 LYS GLY ARG SER LYS SER ASN LEU GLY TRP THR PRO LEU SEQRES 5 B 205 HIS LEU ALA CYS TYR PHE GLY HIS ARG GLN VAL VAL GLN SEQRES 6 B 205 ASP LEU LEU LYS ALA GLY ALA GLU VAL ASN VAL LEU ASN SEQRES 7 B 205 ASP MET GLY ASP THR PRO LEU HIS ARG ALA ALA PHE THR SEQRES 8 B 205 GLY ARG LYS GLU LEU VAL MET LEU LEU LEU GLU TYR ASN SEQRES 9 B 205 ALA ASP THR THR ILE VAL ASN GLY SER GLY GLN THR ALA SEQRES 10 B 205 LYS GLU VAL THR HIS ALA GLU GLU ILE ARG SER MET LEU SEQRES 11 B 205 GLU ALA VAL GLU ARG THR GLN GLN ARG LYS LEU GLU GLU SEQRES 12 B 205 LEU LEU LEU ALA ALA ALA ARG GLU GLY LYS THR THR GLU SEQRES 13 B 205 LEU THR ALA LEU LEU ASN ARG PRO ASN PRO PRO ASP VAL SEQRES 14 B 205 ASN CYS SER ASP GLN LEU GLY ASN THR PRO LEU HIS CYS SEQRES 15 B 205 ALA ALA TYR ARG ALA HIS LYS GLN CYS ALA LEU LYS LEU SEQRES 16 B 205 LEU ARG SER GLY ALA ASP PRO ASN LEU LYS HET GDP A 301 28 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 3 GDP C10 H15 N5 O11 P2 FORMUL 4 HOH *8(H2 O) HELIX 1 AA1 GLY A 20 LYS A 31 1 12 HELIX 2 AA2 PHE A 70 ARG A 79 1 10 HELIX 3 AA3 ALA A 92 THR A 98 1 7 HELIX 4 AA4 THR A 98 SER A 111 1 14 HELIX 5 AA5 ASP A 114 PHE A 118 5 5 HELIX 6 AA6 ALA A 135 LYS A 146 1 12 HELIX 7 AA7 ASN A 161 THR A 178 1 18 HELIX 8 AA8 THR B 3 GLY B 16 1 14 HELIX 9 AA9 ASN B 17 ARG B 30 1 14 HELIX 10 AB1 THR B 50 PHE B 58 1 9 HELIX 11 AB2 HIS B 60 ALA B 70 1 11 HELIX 12 AB3 THR B 83 THR B 91 1 9 HELIX 13 AB4 ARG B 93 TYR B 103 1 11 HELIX 14 AB5 THR B 116 THR B 121 1 6 HELIX 15 AB6 ALA B 123 GLU B 151 1 29 SHEET 1 AA1 6 THR A 47 VAL A 52 0 SHEET 2 AA1 6 ARG A 55 ASP A 63 -1 O ARG A 55 N VAL A 52 SHEET 3 AA1 6 VAL A 7 LEU A 14 1 N VAL A 11 O GLN A 60 SHEET 4 AA1 6 CYS A 83 ASP A 89 1 O VAL A 85 N ILE A 12 SHEET 5 AA1 6 PHE A 120 ASN A 125 1 O LEU A 123 N LEU A 86 SHEET 6 AA1 6 TYR A 151 GLU A 153 1 O PHE A 152 N GLY A 124 CRYST1 80.420 80.420 134.160 90.00 90.00 90.00 P 41 2 2 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 0.012435 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012435 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007454 0.00000