PDB Short entry for 6IF3 HEADER ENDOCYTOSIS 18-SEP-18 6IF3 TITLE COMPLEX STRUCTURE OF RAB35 AND ITS EFFECTOR ACAP2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARF-GAP WITH COILED-COIL, ANK REPEAT AND PH DOMAIN- COMPND 3 CONTAINING PROTEIN 2; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: CENTAURIN-BETA-2,CNT-B2; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RAS-RELATED PROTEIN RAB-35; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: GTP-BINDING PROTEIN RAY,RAS-RELATED PROTEIN RAB-1C; COMPND 11 ENGINEERED: YES; COMPND 12 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: ACAP2, CENTB2, KIAA0041; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: RAB35, RAB1C, RAY; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS RAB35, ACAP2, COMPLEX, CRYATAL STRUCTURE, ENDOCYTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR L.LIN,J.ZHU,R.ZHANG REVDAT 4 22-NOV-23 6IF3 1 LINK REVDAT 3 22-MAY-19 6IF3 1 JRNL REVDAT 2 10-APR-19 6IF3 1 JRNL REVDAT 1 03-APR-19 6IF3 0 JRNL AUTH L.LIN,Y.SHI,M.WANG,C.WANG,J.ZHU,R.ZHANG JRNL TITL RAB35/ACAP2 AND RAB35/RUSC2 COMPLEX STRUCTURES REVEAL JRNL TITL 2 MOLECULAR BASIS FOR EFFECTOR RECOGNITION BY RAB35 GTPASE. JRNL REF STRUCTURE V. 27 729 2019 JRNL REFN ISSN 0969-2126 JRNL PMID 30905672 JRNL DOI 10.1016/J.STR.2019.02.008 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 54479 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 2759 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 28.0536 - 4.0677 1.00 2876 153 0.1684 0.2024 REMARK 3 2 4.0677 - 3.2302 1.00 2768 133 0.1434 0.1695 REMARK 3 3 3.2302 - 2.8223 1.00 2695 148 0.1506 0.1773 REMARK 3 4 2.8223 - 2.5644 1.00 2686 170 0.1624 0.1845 REMARK 3 5 2.5644 - 2.3807 1.00 2708 137 0.1650 0.1972 REMARK 3 6 2.3807 - 2.2404 1.00 2648 134 0.1608 0.1961 REMARK 3 7 2.2404 - 2.1283 1.00 2676 138 0.1666 0.1921 REMARK 3 8 2.1283 - 2.0357 1.00 2672 137 0.1639 0.2095 REMARK 3 9 2.0357 - 1.9573 1.00 2671 138 0.1725 0.1841 REMARK 3 10 1.9573 - 1.8898 1.00 2641 140 0.1733 0.2123 REMARK 3 11 1.8898 - 1.8307 1.00 2644 136 0.1872 0.2375 REMARK 3 12 1.8307 - 1.7784 1.00 2627 147 0.2003 0.2505 REMARK 3 13 1.7784 - 1.7316 1.00 2632 148 0.2078 0.2591 REMARK 3 14 1.7316 - 1.6893 1.00 2668 144 0.2119 0.2569 REMARK 3 15 1.6893 - 1.6509 1.00 2618 129 0.2192 0.2760 REMARK 3 16 1.6509 - 1.6158 0.99 2571 159 0.2396 0.2947 REMARK 3 17 1.6158 - 1.5835 0.97 2546 127 0.2529 0.2927 REMARK 3 18 1.5835 - 1.5536 0.88 2328 132 0.2763 0.3113 REMARK 3 19 1.5536 - 1.5259 0.82 2167 116 0.2979 0.3370 REMARK 3 20 1.5259 - 1.5000 0.71 1878 93 0.3230 0.3538 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.600 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.55 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.04 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 : 0.011 2736 REMARK 3 ANGLE : 1.255 3724 REMARK 3 CHIRALITY : 0.057 424 REMARK 3 PLANARITY : 0.007 485 REMARK 3 DIHEDRAL : 17.529 1017 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 605 THROUGH 627 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.3041 45.9180 17.9145 REMARK 3 T TENSOR REMARK 3 T11: 0.1330 T22: 0.1182 REMARK 3 T33: 0.1567 T12: 0.0028 REMARK 3 T13: -0.0019 T23: -0.0567 REMARK 3 L TENSOR REMARK 3 L11: 7.3914 L22: 4.2633 REMARK 3 L33: 6.3957 L12: 0.2799 REMARK 3 L13: 1.6572 L23: -3.5403 REMARK 3 S TENSOR REMARK 3 S11: -0.0623 S12: -0.2604 S13: 0.2449 REMARK 3 S21: 0.2701 S22: -0.0074 S23: -0.0589 REMARK 3 S31: -0.2844 S32: 0.0586 S33: 0.0621 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 628 THROUGH 637 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.1472 37.9661 22.1799 REMARK 3 T TENSOR REMARK 3 T11: 0.1827 T22: 0.1279 REMARK 3 T33: 0.1332 T12: -0.0074 REMARK 3 T13: 0.0182 T23: 0.0088 REMARK 3 L TENSOR REMARK 3 L11: 4.7825 L22: 4.3620 REMARK 3 L33: 8.7329 L12: -3.2294 REMARK 3 L13: 0.2040 L23: -0.1435 REMARK 3 S TENSOR REMARK 3 S11: -0.3330 S12: -0.0539 S13: -0.1224 REMARK 3 S21: 0.4150 S22: 0.1032 S23: 0.1176 REMARK 3 S31: 0.1355 S32: 0.0734 S33: 0.1541 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 638 THROUGH 695 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.1138 35.6502 8.4218 REMARK 3 T TENSOR REMARK 3 T11: 0.1182 T22: 0.1328 REMARK 3 T33: 0.1202 T12: -0.0042 REMARK 3 T13: 0.0155 T23: -0.0128 REMARK 3 L TENSOR REMARK 3 L11: 1.3589 L22: 2.3847 REMARK 3 L33: 2.4888 L12: -0.0481 REMARK 3 L13: 0.0163 L23: 0.2734 REMARK 3 S TENSOR REMARK 3 S11: -0.0074 S12: 0.0206 S13: 0.0377 REMARK 3 S21: 0.0823 S22: -0.0027 S23: 0.0162 REMARK 3 S31: 0.0138 S32: 0.0084 S33: 0.0186 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 696 THROUGH 709 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.0379 25.1292 4.3302 REMARK 3 T TENSOR REMARK 3 T11: 0.2158 T22: 0.1209 REMARK 3 T33: 0.1087 T12: -0.0270 REMARK 3 T13: 0.0046 T23: -0.0047 REMARK 3 L TENSOR REMARK 3 L11: 6.6149 L22: 6.5265 REMARK 3 L33: 8.2157 L12: 1.1240 REMARK 3 L13: -3.7264 L23: -0.9620 REMARK 3 S TENSOR REMARK 3 S11: -0.2737 S12: 0.4115 S13: -0.0007 REMARK 3 S21: -0.2095 S22: 0.0393 S23: 0.1893 REMARK 3 S31: 0.3621 S32: -0.3199 S33: 0.2468 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 710 THROUGH 738 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.3935 24.9009 -5.9817 REMARK 3 T TENSOR REMARK 3 T11: 0.1349 T22: 0.1495 REMARK 3 T33: 0.1099 T12: -0.0183 REMARK 3 T13: 0.0126 T23: -0.0261 REMARK 3 L TENSOR REMARK 3 L11: 4.9549 L22: 6.2131 REMARK 3 L33: 3.2310 L12: -2.7895 REMARK 3 L13: 0.6063 L23: 0.3599 REMARK 3 S TENSOR REMARK 3 S11: -0.0369 S12: 0.0856 S13: -0.3277 REMARK 3 S21: 0.1130 S22: -0.0211 S23: 0.0493 REMARK 3 S31: 0.1532 S32: 0.1093 S33: 0.0461 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 739 THROUGH 757 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.9853 27.1752 -6.8363 REMARK 3 T TENSOR REMARK 3 T11: 0.1785 T22: 0.2660 REMARK 3 T33: 0.2752 T12: -0.0108 REMARK 3 T13: 0.0269 T23: -0.0529 REMARK 3 L TENSOR REMARK 3 L11: 4.7798 L22: 1.9550 REMARK 3 L33: 5.9989 L12: 1.1555 REMARK 3 L13: -0.0104 L23: -2.6995 REMARK 3 S TENSOR REMARK 3 S11: -0.0706 S12: 0.1998 S13: -0.6184 REMARK 3 S21: -0.2732 S22: 0.1189 S23: -0.3310 REMARK 3 S31: 0.2667 S32: 0.3684 S33: 0.0637 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 758 THROUGH 769 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.3045 41.8542 -6.1466 REMARK 3 T TENSOR REMARK 3 T11: 0.3757 T22: 0.6036 REMARK 3 T33: 0.5403 T12: 0.0623 REMARK 3 T13: 0.0540 T23: -0.0664 REMARK 3 L TENSOR REMARK 3 L11: 5.4280 L22: 5.0653 REMARK 3 L33: 7.6520 L12: -5.1269 REMARK 3 L13: -5.7683 L23: 4.9660 REMARK 3 S TENSOR REMARK 3 S11: 0.9597 S12: 0.2078 S13: 1.6827 REMARK 3 S21: -0.6184 S22: -0.5498 S23: -0.4172 REMARK 3 S31: -1.0053 S32: -1.3294 S33: -0.5682 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 2 THROUGH 30 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.9856 15.0619 -18.0824 REMARK 3 T TENSOR REMARK 3 T11: 0.1825 T22: 0.1568 REMARK 3 T33: 0.0884 T12: 0.0186 REMARK 3 T13: 0.0303 T23: -0.0304 REMARK 3 L TENSOR REMARK 3 L11: 4.4103 L22: 4.1713 REMARK 3 L33: 2.1586 L12: -2.7839 REMARK 3 L13: 2.0290 L23: -1.4731 REMARK 3 S TENSOR REMARK 3 S11: -0.1338 S12: -0.1352 S13: 0.0486 REMARK 3 S21: 0.1262 S22: 0.0253 S23: -0.0767 REMARK 3 S31: 0.0601 S32: -0.0853 S33: 0.1192 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 31 THROUGH 64 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.8339 14.4451 -15.8791 REMARK 3 T TENSOR REMARK 3 T11: 0.1652 T22: 0.1831 REMARK 3 T33: 0.1529 T12: 0.0008 REMARK 3 T13: 0.0128 T23: 0.0033 REMARK 3 L TENSOR REMARK 3 L11: 1.6289 L22: 3.9432 REMARK 3 L33: 0.8443 L12: -1.8893 REMARK 3 L13: 0.0726 L23: 0.6944 REMARK 3 S TENSOR REMARK 3 S11: -0.0058 S12: -0.0522 S13: 0.0294 REMARK 3 S21: 0.1074 S22: -0.0529 S23: 0.0238 REMARK 3 S31: 0.0863 S32: -0.1077 S33: 0.0531 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 65 THROUGH 82 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.1797 29.7367 -18.7320 REMARK 3 T TENSOR REMARK 3 T11: 0.1718 T22: 0.1499 REMARK 3 T33: 0.1438 T12: -0.0106 REMARK 3 T13: 0.0157 T23: 0.0294 REMARK 3 L TENSOR REMARK 3 L11: 5.0004 L22: 5.2385 REMARK 3 L33: 2.9292 L12: -4.8753 REMARK 3 L13: -3.9579 L23: 3.8686 REMARK 3 S TENSOR REMARK 3 S11: 0.0788 S12: 0.1848 S13: 0.2422 REMARK 3 S21: -0.1374 S22: 0.0328 S23: -0.2074 REMARK 3 S31: -0.1491 S32: -0.0378 S33: -0.1485 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 83 THROUGH 109 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.4506 26.0365 -31.2741 REMARK 3 T TENSOR REMARK 3 T11: 0.2549 T22: 0.1642 REMARK 3 T33: 0.1363 T12: -0.0034 REMARK 3 T13: -0.0032 T23: 0.0070 REMARK 3 L TENSOR REMARK 3 L11: 8.7903 L22: 1.7628 REMARK 3 L33: 3.3215 L12: 1.6624 REMARK 3 L13: 3.4988 L23: 1.3742 REMARK 3 S TENSOR REMARK 3 S11: -0.3462 S12: 0.2634 S13: 0.3575 REMARK 3 S21: -0.4878 S22: 0.0987 S23: 0.0635 REMARK 3 S31: -0.4309 S32: 0.0178 S33: 0.2635 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 110 THROUGH 142 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.8756 17.8862 -35.8568 REMARK 3 T TENSOR REMARK 3 T11: 0.2408 T22: 0.1922 REMARK 3 T33: 0.1572 T12: -0.0053 REMARK 3 T13: -0.0090 T23: -0.0195 REMARK 3 L TENSOR REMARK 3 L11: 2.7261 L22: 2.2145 REMARK 3 L33: 3.5742 L12: -0.8839 REMARK 3 L13: -1.4565 L23: 0.4259 REMARK 3 S TENSOR REMARK 3 S11: -0.1248 S12: 0.5250 S13: -0.0657 REMARK 3 S21: -0.3380 S22: -0.0616 S23: 0.0784 REMARK 3 S31: -0.0786 S32: -0.2810 S33: 0.1704 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 143 THROUGH 178 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.5950 10.0483 -27.0799 REMARK 3 T TENSOR REMARK 3 T11: 0.2448 T22: 0.1666 REMARK 3 T33: 0.1927 T12: 0.0445 REMARK 3 T13: 0.0236 T23: -0.0320 REMARK 3 L TENSOR REMARK 3 L11: 6.3212 L22: 1.8839 REMARK 3 L33: 2.5960 L12: 0.9087 REMARK 3 L13: 1.0147 L23: 0.3674 REMARK 3 S TENSOR REMARK 3 S11: 0.0212 S12: 0.0490 S13: -0.3420 REMARK 3 S21: 0.0266 S22: -0.0354 S23: -0.1055 REMARK 3 S31: 0.2173 S32: 0.2052 S33: 0.0057 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 6IF3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1300009092. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-NOV-16 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 : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54675 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 96.7 REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : 0.11700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.58400 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3TW8, 3JUE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: POTASSIUM SODIUM TARTRATE, PEG 3350, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 22.37050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.00400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.73400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 72.00400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.37050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.73400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 597 REMARK 465 PRO A 598 REMARK 465 GLY A 599 REMARK 465 SER A 600 REMARK 465 SER A 601 REMARK 465 LYS A 602 REMARK 465 HIS A 603 REMARK 465 LEU A 604 REMARK 465 GLY A 740 REMARK 465 LEU A 741 REMARK 465 TYR A 742 REMARK 465 GLY A 743 REMARK 465 GLN A 744 REMARK 465 PRO A 745 REMARK 465 GLY A 746 REMARK 465 GLY B -5 REMARK 465 PRO B -4 REMARK 465 GLY B -3 REMARK 465 SER B -2 REMARK 465 GLU B -1 REMARK 465 PHE B 0 REMARK 465 MET B 1 REMARK 465 GLN B 179 REMARK 465 GLN B 180 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 ARG A 736 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 737 CG CD OE1 OE2 REMARK 470 GLU A 739 CG CD OE1 OE2 REMARK 470 ASP A 747 CG OD1 OD2 REMARK 470 GLU A 748 CG CD OE1 OE2 REMARK 470 GLU A 766 CG CD OE1 OE2 REMARK 470 GLU B 126 CG CD OE1 OE2 REMARK 470 ARG B 170 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 178 CG CD CE NZ 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 B 461 O HOH B 476 1.97 REMARK 500 O HOH A 930 O HOH B 497 2.09 REMARK 500 O HOH A 957 O HOH A 979 2.10 REMARK 500 O HOH B 448 O HOH B 471 2.12 REMARK 500 O HOH A 962 O HOH A 968 2.15 REMARK 500 OD1 ASN B 175 O HOH B 301 2.17 REMARK 500 NH2 ARG A 770 O HOH A 801 2.17 REMARK 500 O HOH B 339 O HOH B 477 2.19 REMARK 500 OE1 GLU B 166 O HOH B 302 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 949 O HOH A 973 4465 2.16 REMARK 500 NH1 ARG A 696 O GLU A 766 4565 2.18 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 123 16.38 -140.41 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 988 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH A 989 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH A 990 DISTANCE = 7.06 ANGSTROMS REMARK 525 HOH A 991 DISTANCE = 7.48 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 B 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 22 OG REMARK 620 2 THR B 40 OG1 83.6 REMARK 620 3 GTP B 201 O2G 175.1 92.3 REMARK 620 4 GTP B 201 O2B 90.2 173.7 93.8 REMARK 620 5 HOH B 322 O 87.1 89.2 95.4 91.5 REMARK 620 6 HOH B 332 O 87.6 90.8 89.9 87.9 174.7 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 B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 202 DBREF 6IF3 A 601 770 UNP Q15057 ACAP2_HUMAN 601 770 DBREF 6IF3 B 1 180 UNP Q15286 RAB35_HUMAN 1 180 SEQADV 6IF3 GLY A 597 UNP Q15057 EXPRESSION TAG SEQADV 6IF3 PRO A 598 UNP Q15057 EXPRESSION TAG SEQADV 6IF3 GLY A 599 UNP Q15057 EXPRESSION TAG SEQADV 6IF3 SER A 600 UNP Q15057 EXPRESSION TAG SEQADV 6IF3 GLY B -5 UNP Q15286 EXPRESSION TAG SEQADV 6IF3 PRO B -4 UNP Q15286 EXPRESSION TAG SEQADV 6IF3 GLY B -3 UNP Q15286 EXPRESSION TAG SEQADV 6IF3 SER B -2 UNP Q15286 EXPRESSION TAG SEQADV 6IF3 GLU B -1 UNP Q15286 EXPRESSION TAG SEQADV 6IF3 PHE B 0 UNP Q15286 EXPRESSION TAG SEQADV 6IF3 LEU B 67 UNP Q15286 GLN 67 ENGINEERED MUTATION SEQRES 1 A 174 GLY PRO GLY SER SER LYS HIS LEU ASN PRO GLY LEU GLN SEQRES 2 A 174 LEU TYR ARG ALA SER TYR GLU LYS ASN LEU PRO LYS MET SEQRES 3 A 174 ALA GLU ALA LEU ALA HIS GLY ALA ASP VAL ASN TRP ALA SEQRES 4 A 174 ASN SER GLU GLU ASN LYS ALA THR PRO LEU ILE GLN ALA SEQRES 5 A 174 VAL LEU GLY GLY SER LEU VAL THR CYS GLU PHE LEU LEU SEQRES 6 A 174 GLN ASN GLY ALA ASN VAL ASN GLN ARG ASP VAL GLN GLY SEQRES 7 A 174 ARG GLY PRO LEU HIS HIS ALA THR VAL LEU GLY HIS THR SEQRES 8 A 174 GLY GLN VAL CYS LEU PHE LEU LYS ARG GLY ALA ASN GLN SEQRES 9 A 174 HIS ALA THR ASP GLU GLU GLY LYS ASP PRO LEU SER ILE SEQRES 10 A 174 ALA VAL GLU ALA ALA ASN ALA ASP ILE VAL THR LEU LEU SEQRES 11 A 174 ARG LEU ALA ARG MET ASN GLU GLU MET ARG GLU SER GLU SEQRES 12 A 174 GLY LEU TYR GLY GLN PRO GLY ASP GLU THR TYR GLN ASP SEQRES 13 A 174 ILE PHE ARG ASP PHE SER GLN MET ALA SER ASN ASN PRO SEQRES 14 A 174 GLU LYS LEU ASN ARG SEQRES 1 B 186 GLY PRO GLY SER GLU PHE MET ALA ARG ASP TYR ASP HIS SEQRES 2 B 186 LEU PHE LYS LEU LEU ILE ILE GLY ASP SER GLY VAL GLY SEQRES 3 B 186 LYS SER SER LEU LEU LEU ARG PHE ALA ASP ASN THR PHE SEQRES 4 B 186 SER GLY SER TYR ILE THR THR ILE GLY VAL ASP PHE LYS SEQRES 5 B 186 ILE ARG THR VAL GLU ILE ASN GLY GLU LYS VAL LYS LEU SEQRES 6 B 186 GLN ILE TRP ASP THR ALA GLY LEU GLU ARG PHE ARG THR SEQRES 7 B 186 ILE THR SER THR TYR TYR ARG GLY THR HIS GLY VAL ILE SEQRES 8 B 186 VAL VAL TYR ASP VAL THR SER ALA GLU SER PHE VAL ASN SEQRES 9 B 186 VAL LYS ARG TRP LEU HIS GLU ILE ASN GLN ASN CYS ASP SEQRES 10 B 186 ASP VAL CYS ARG ILE LEU VAL GLY ASN LYS ASN ASP ASP SEQRES 11 B 186 PRO GLU ARG LYS VAL VAL GLU THR GLU ASP ALA TYR LYS SEQRES 12 B 186 PHE ALA GLY GLN MET GLY ILE GLN LEU PHE GLU THR SER SEQRES 13 B 186 ALA LYS GLU ASN VAL ASN VAL GLU GLU MET PHE ASN CYS SEQRES 14 B 186 ILE THR GLU LEU VAL LEU ARG ALA LYS LYS ASP ASN LEU SEQRES 15 B 186 ALA LYS GLN GLN HET GTP B 201 32 HET MG B 202 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 3 GTP C10 H16 N5 O14 P3 FORMUL 4 MG MG 2+ FORMUL 5 HOH *390(H2 O) HELIX 1 AA1 ASN A 605 GLU A 616 1 12 HELIX 2 AA2 ASN A 618 HIS A 628 1 11 HELIX 3 AA3 THR A 643 GLY A 652 1 10 HELIX 4 AA4 SER A 653 ASN A 663 1 11 HELIX 5 AA5 GLY A 676 GLY A 685 1 10 HELIX 6 AA6 HIS A 686 ARG A 696 1 11 HELIX 7 AA7 ASP A 709 ALA A 717 1 9 HELIX 8 AA8 ASN A 719 SER A 738 1 20 HELIX 9 AA9 ASP A 752 SER A 758 1 7 HELIX 10 AB1 GLY B 20 ASN B 31 1 12 HELIX 11 AB2 LEU B 67 ARG B 71 5 5 HELIX 12 AB3 ILE B 73 ARG B 79 1 7 HELIX 13 AB4 SER B 92 ASN B 98 1 7 HELIX 14 AB5 ASN B 98 CYS B 110 1 13 HELIX 15 AB6 ASP B 124 LYS B 128 5 5 HELIX 16 AB7 GLU B 131 GLY B 143 1 13 HELIX 17 AB8 ASN B 156 ASP B 174 1 19 SHEET 1 AA1 6 VAL B 43 ILE B 52 0 SHEET 2 AA1 6 GLU B 55 THR B 64 -1 O LEU B 59 N ARG B 48 SHEET 3 AA1 6 HIS B 7 GLY B 15 1 N HIS B 7 O LYS B 58 SHEET 4 AA1 6 GLY B 83 ASP B 89 1 O ILE B 85 N LEU B 12 SHEET 5 AA1 6 CYS B 114 ASN B 120 1 O ASN B 120 N TYR B 88 SHEET 6 AA1 6 GLN B 145 GLU B 148 1 O GLN B 145 N LEU B 117 LINK OG SER B 22 MG MG B 202 1555 1555 2.16 LINK OG1 THR B 40 MG MG B 202 1555 1555 2.07 LINK O2G GTP B 201 MG MG B 202 1555 1555 2.01 LINK O2B GTP B 201 MG MG B 202 1555 1555 2.09 LINK MG MG B 202 O HOH B 322 1555 1555 2.07 LINK MG MG B 202 O HOH B 332 1555 1555 2.09 SITE 1 AC1 26 SER B 17 GLY B 18 VAL B 19 GLY B 20 SITE 2 AC1 26 LYS B 21 SER B 22 SER B 23 PHE B 33 SITE 3 AC1 26 GLY B 35 TYR B 37 THR B 40 GLY B 66 SITE 4 AC1 26 ASN B 120 LYS B 121 ASP B 123 SER B 150 SITE 5 AC1 26 ALA B 151 LYS B 152 MG B 202 HOH B 301 SITE 6 AC1 26 HOH B 322 HOH B 327 HOH B 332 HOH B 333 SITE 7 AC1 26 HOH B 410 HOH B 437 SITE 1 AC2 5 SER B 22 THR B 40 GTP B 201 HOH B 322 SITE 2 AC2 5 HOH B 332 CRYST1 44.741 53.468 144.008 90.00 90.00 90.00 P 21 21 21 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 0.022351 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018703 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006944 0.00000