HEADER OXIDOREDUCTASE 30-NOV-17 6F4T TITLE HUMAN JMJD5 (W414C) IN COMPLEX WITH MN(II), NOG AND RCCD1 (139-143) TITLE 2 (COMPLEX-5) COMPND MOL_ID: 1; COMPND 2 MOLECULE: JMJC DOMAIN-CONTAINING PROTEIN 5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, UNP RESIDUES 183-416; COMPND 5 SYNONYM: JUMONJI DOMAIN-CONTAINING PROTEIN 5,LYSINE-SPECIFIC COMPND 6 DEMETHYLASE 8; COMPND 7 EC: 1.14.11.47; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 OTHER_DETAILS: FRAGMENT: 183-416; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: RCC1 DOMAIN-CONTAINING PROTEIN 1; COMPND 13 CHAIN: B; COMPND 14 FRAGMENT: UNP RESIDUES 139-143; COMPND 15 ENGINEERED: YES; COMPND 16 OTHER_DETAILS: FRAGMENT: 139-143 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: KDM8, JMJD5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PNIC28 BSA4; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606 KEYWDS OXIDOREDUCTASE, NON-HEME, IRON, 2-OXOGLUTARATE, DIOXYGENASE, JMJC, KEYWDS 2 JMJC DOMAIN, LYSINE-SPECIFIC DEMETHYLASE 8, JMJC DOMAIN-CONTAINING KEYWDS 3 PROTEIN 5, ARGINYL C-3 HYDROXYLASE, JMJD5, KDM8, OXYGENASE, HYPOXIA, KEYWDS 4 DNA-BINDING, METAL-BINDING, TRANSLATION, DSBH, FACIAL TRIAD, KEYWDS 5 CYTOPLASM, JMJC HYDROXYLASE, JMJC DEMETHYLASE, KDMS, POST- KEYWDS 6 TRANSLATIONAL MODIFICATIONS, PTM, BETA-HYDROXYLATION, HYDROXYLATION, KEYWDS 7 ARGININE HYDROXYLATION, RCC1 DOMAIN-CONTAINING PROTEIN 1, RCCD1, KEYWDS 8 REGULATOR OF CHROMOSOME CONDENSATION, 40S RIBOSOMAL PROTEIN S6, KEYWDS 9 RPS6, RIBOSOME BIOGENESIS, TRANSCRIPTION, EPIGENETIC REGULATION, KEYWDS 10 SIGNALING, DEVELOPMENT, CELL STRUCTURE, TRANSCRIPTION KEYWDS 11 ACTIVATOR/INHIBITOR, PHOSPHORYLATION, CANCER, POLYMORPHISM EXPDTA X-RAY DIFFRACTION AUTHOR R.CHOWDHURY,M.S.ISLAM,C.J.SCHOFIELD REVDAT 2 17-JAN-24 6F4T 1 LINK REVDAT 1 04-APR-18 6F4T 0 JRNL AUTH S.E.WILKINS,S.ISLAM,J.M.GANNON,S.MARKOLOVIC,R.J.HOPKINSON, JRNL AUTH 2 W.GE,C.J.SCHOFIELD,R.CHOWDHURY JRNL TITL JMJD5 IS A HUMAN ARGINYL C-3 HYDROXYLASE. JRNL REF NAT COMMUN V. 9 1180 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 29563586 JRNL DOI 10.1038/S41467-018-03410-W REMARK 2 REMARK 2 RESOLUTION. 1.22 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) : 1.22 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.23 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 75238 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.142 REMARK 3 R VALUE (WORKING SET) : 0.141 REMARK 3 FREE R VALUE : 0.154 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 3767 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 39.2545 - 3.6591 0.97 2792 156 0.1460 0.1503 REMARK 3 2 3.6591 - 2.9046 0.98 2673 154 0.1286 0.1451 REMARK 3 3 2.9046 - 2.5375 0.99 2702 125 0.1328 0.1606 REMARK 3 4 2.5375 - 2.3055 0.98 2656 132 0.1267 0.1487 REMARK 3 5 2.3055 - 2.1403 0.98 2627 143 0.1227 0.1458 REMARK 3 6 2.1403 - 2.0141 0.99 2646 156 0.1207 0.1293 REMARK 3 7 2.0141 - 1.9133 0.99 2645 138 0.1211 0.1273 REMARK 3 8 1.9133 - 1.8300 1.00 2639 139 0.1283 0.1319 REMARK 3 9 1.8300 - 1.7595 1.00 2665 136 0.1273 0.1433 REMARK 3 10 1.7595 - 1.6988 1.00 2642 148 0.1298 0.1259 REMARK 3 11 1.6988 - 1.6457 1.00 2648 142 0.1289 0.1428 REMARK 3 12 1.6457 - 1.5986 1.00 2625 152 0.1331 0.1395 REMARK 3 13 1.5986 - 1.5566 1.00 2647 154 0.1387 0.1749 REMARK 3 14 1.5566 - 1.5186 1.00 2650 123 0.1450 0.1743 REMARK 3 15 1.5186 - 1.4841 1.00 2624 155 0.1476 0.1724 REMARK 3 16 1.4841 - 1.4525 1.00 2623 130 0.1541 0.1743 REMARK 3 17 1.4525 - 1.4234 1.00 2674 137 0.1627 0.1704 REMARK 3 18 1.4234 - 1.3966 1.00 2622 135 0.1652 0.1702 REMARK 3 19 1.3966 - 1.3716 1.00 2640 130 0.1759 0.1826 REMARK 3 20 1.3716 - 1.3484 1.00 2644 141 0.1884 0.2122 REMARK 3 21 1.3484 - 1.3266 1.00 2582 147 0.1991 0.2328 REMARK 3 22 1.3266 - 1.3062 1.00 2672 133 0.2183 0.2269 REMARK 3 23 1.3062 - 1.2870 1.00 2602 150 0.2253 0.2390 REMARK 3 24 1.2870 - 1.2689 1.00 2622 140 0.2389 0.2753 REMARK 3 25 1.2689 - 1.2517 1.00 2639 119 0.2711 0.2460 REMARK 3 26 1.2517 - 1.2355 1.00 2656 122 0.2872 0.3130 REMARK 3 27 1.2355 - 1.2200 1.00 2614 130 0.3178 0.3613 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.41 REMARK 3 B_SOL : 54.10 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.88000 REMARK 3 B22 (A**2) : -1.27000 REMARK 3 B33 (A**2) : 5.14000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.018 2288 REMARK 3 ANGLE : 1.511 3147 REMARK 3 CHIRALITY : 0.106 323 REMARK 3 PLANARITY : 0.012 427 REMARK 3 DIHEDRAL : 16.002 868 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 12 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 182:211) REMARK 3 ORIGIN FOR THE GROUP (A): -24.8699 21.7830 -19.8526 REMARK 3 T TENSOR REMARK 3 T11: 0.1552 T22: 0.2243 REMARK 3 T33: 0.2383 T12: 0.0482 REMARK 3 T13: 0.0399 T23: 0.0411 REMARK 3 L TENSOR REMARK 3 L11: 0.4195 L22: 0.2723 REMARK 3 L33: 0.5219 L12: -0.3304 REMARK 3 L13: -0.3308 L23: -0.0506 REMARK 3 S TENSOR REMARK 3 S11: 0.0001 S12: 0.0188 S13: 0.2697 REMARK 3 S21: 0.0750 S22: 0.0879 S23: 0.2285 REMARK 3 S31: -0.1933 S32: -0.2765 S33: 0.0497 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 212:230) REMARK 3 ORIGIN FOR THE GROUP (A): -8.5664 10.6131 -3.2113 REMARK 3 T TENSOR REMARK 3 T11: 0.2541 T22: 0.2222 REMARK 3 T33: 0.1642 T12: 0.0358 REMARK 3 T13: 0.0051 T23: -0.0311 REMARK 3 L TENSOR REMARK 3 L11: 0.2642 L22: 0.1434 REMARK 3 L33: 0.4383 L12: 0.2045 REMARK 3 L13: -0.0991 L23: -0.0591 REMARK 3 S TENSOR REMARK 3 S11: -0.0544 S12: -0.1623 S13: 0.1388 REMARK 3 S21: 0.1944 S22: 0.1374 S23: -0.0943 REMARK 3 S31: -0.1762 S32: -0.0466 S33: 0.0021 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 231:254) REMARK 3 ORIGIN FOR THE GROUP (A): 3.2970 4.4061 -22.2311 REMARK 3 T TENSOR REMARK 3 T11: 0.2006 T22: 0.2057 REMARK 3 T33: 0.1781 T12: 0.0284 REMARK 3 T13: 0.0314 T23: 0.0237 REMARK 3 L TENSOR REMARK 3 L11: 0.9821 L22: 0.5504 REMARK 3 L33: 0.3374 L12: -0.3186 REMARK 3 L13: 0.3583 L23: 0.2951 REMARK 3 S TENSOR REMARK 3 S11: 0.0705 S12: 0.2469 S13: 0.0501 REMARK 3 S21: -0.1884 S22: -0.1333 S23: -0.0692 REMARK 3 S31: 0.0116 S32: 0.1786 S33: 0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 255:277) REMARK 3 ORIGIN FOR THE GROUP (A): 4.6951 7.5956 -14.6053 REMARK 3 T TENSOR REMARK 3 T11: 0.1413 T22: 0.1597 REMARK 3 T33: 0.1882 T12: -0.0108 REMARK 3 T13: 0.0008 T23: 0.0252 REMARK 3 L TENSOR REMARK 3 L11: 0.3439 L22: 0.8651 REMARK 3 L33: 0.9791 L12: -0.7230 REMARK 3 L13: 0.0377 L23: -0.5602 REMARK 3 S TENSOR REMARK 3 S11: 0.0013 S12: 0.1643 S13: 0.1272 REMARK 3 S21: 0.0695 S22: -0.0970 S23: -0.2016 REMARK 3 S31: -0.0258 S32: 0.2110 S33: -0.0003 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 278:305) REMARK 3 ORIGIN FOR THE GROUP (A): -19.4347 4.6155 -13.0458 REMARK 3 T TENSOR REMARK 3 T11: 0.1870 T22: 0.1991 REMARK 3 T33: 0.2404 T12: -0.0144 REMARK 3 T13: 0.0215 T23: 0.0453 REMARK 3 L TENSOR REMARK 3 L11: 0.3100 L22: 0.4544 REMARK 3 L33: 0.0600 L12: -0.0706 REMARK 3 L13: -0.1504 L23: -0.0990 REMARK 3 S TENSOR REMARK 3 S11: -0.0697 S12: -0.1116 S13: -0.2870 REMARK 3 S21: 0.1203 S22: 0.1143 S23: 0.2531 REMARK 3 S31: 0.0986 S32: -0.1576 S33: 0.0036 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 306:312) REMARK 3 ORIGIN FOR THE GROUP (A): -9.3228 6.8672 -17.1222 REMARK 3 T TENSOR REMARK 3 T11: 0.1456 T22: 0.1306 REMARK 3 T33: 0.1753 T12: 0.0042 REMARK 3 T13: -0.0081 T23: -0.0036 REMARK 3 L TENSOR REMARK 3 L11: 0.0510 L22: 0.0883 REMARK 3 L33: 0.0476 L12: -0.1100 REMARK 3 L13: 0.0344 L23: -0.0594 REMARK 3 S TENSOR REMARK 3 S11: 0.0483 S12: 0.0098 S13: -0.0605 REMARK 3 S21: 0.0045 S22: 0.0306 S23: 0.0677 REMARK 3 S31: 0.0195 S32: 0.0426 S33: 0.0001 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 313:325) REMARK 3 ORIGIN FOR THE GROUP (A): -6.2637 13.2785 -25.9522 REMARK 3 T TENSOR REMARK 3 T11: 0.1407 T22: 0.1380 REMARK 3 T33: 0.1405 T12: -0.0106 REMARK 3 T13: -0.0143 T23: -0.0060 REMARK 3 L TENSOR REMARK 3 L11: 0.2888 L22: 0.3302 REMARK 3 L33: 0.5279 L12: -0.1406 REMARK 3 L13: -0.3200 L23: -0.2616 REMARK 3 S TENSOR REMARK 3 S11: 0.0564 S12: 0.0925 S13: -0.1081 REMARK 3 S21: -0.0127 S22: 0.0154 S23: -0.0778 REMARK 3 S31: 0.0462 S32: 0.0824 S33: -0.0000 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 326:341) REMARK 3 ORIGIN FOR THE GROUP (A): -9.9543 18.6101 -20.0712 REMARK 3 T TENSOR REMARK 3 T11: 0.1331 T22: 0.1169 REMARK 3 T33: 0.1126 T12: 0.0026 REMARK 3 T13: 0.0050 T23: 0.0018 REMARK 3 L TENSOR REMARK 3 L11: 0.2061 L22: 0.2626 REMARK 3 L33: 0.3197 L12: -0.1385 REMARK 3 L13: -0.1783 L23: -0.2587 REMARK 3 S TENSOR REMARK 3 S11: 0.0214 S12: -0.0250 S13: 0.0080 REMARK 3 S21: 0.0921 S22: 0.0638 S23: 0.0452 REMARK 3 S31: -0.0557 S32: -0.0203 S33: 0.0007 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN A AND RESID 342:365) REMARK 3 ORIGIN FOR THE GROUP (A): -7.7077 14.3188 -38.0593 REMARK 3 T TENSOR REMARK 3 T11: 0.1887 T22: 0.1773 REMARK 3 T33: 0.1390 T12: -0.0129 REMARK 3 T13: 0.0057 T23: -0.0326 REMARK 3 L TENSOR REMARK 3 L11: 0.5606 L22: 0.4650 REMARK 3 L33: 0.8189 L12: -0.0282 REMARK 3 L13: -0.5836 L23: -0.5356 REMARK 3 S TENSOR REMARK 3 S11: -0.0630 S12: 0.1830 S13: -0.1039 REMARK 3 S21: -0.2564 S22: 0.0100 S23: -0.0042 REMARK 3 S31: 0.0356 S32: -0.0742 S33: 0.0001 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN A AND RESID 366:381) REMARK 3 ORIGIN FOR THE GROUP (A): -2.1117 24.7022 -39.1846 REMARK 3 T TENSOR REMARK 3 T11: 0.1989 T22: 0.1918 REMARK 3 T33: 0.1465 T12: 0.0134 REMARK 3 T13: 0.0489 T23: 0.0141 REMARK 3 L TENSOR REMARK 3 L11: 0.1397 L22: 0.4112 REMARK 3 L33: 0.1588 L12: 0.0364 REMARK 3 L13: -0.2377 L23: 0.1831 REMARK 3 S TENSOR REMARK 3 S11: 0.1472 S12: 0.1263 S13: 0.1147 REMARK 3 S21: -0.0453 S22: -0.0233 S23: -0.0833 REMARK 3 S31: -0.2363 S32: 0.0253 S33: 0.0019 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN A AND RESID 382:399) REMARK 3 ORIGIN FOR THE GROUP (A): -14.4111 19.1237 -23.0778 REMARK 3 T TENSOR REMARK 3 T11: 0.1420 T22: 0.1331 REMARK 3 T33: 0.1414 T12: 0.0044 REMARK 3 T13: 0.0067 T23: 0.0018 REMARK 3 L TENSOR REMARK 3 L11: 0.4325 L22: 0.2742 REMARK 3 L33: 0.3238 L12: -0.1619 REMARK 3 L13: -0.2342 L23: -0.3195 REMARK 3 S TENSOR REMARK 3 S11: 0.0113 S12: 0.0017 S13: 0.0796 REMARK 3 S21: 0.0584 S22: 0.0699 S23: 0.0946 REMARK 3 S31: -0.1045 S32: -0.1064 S33: 0.0033 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: (CHAIN A AND RESID 400:416) REMARK 3 ORIGIN FOR THE GROUP (A): -10.4638 13.2728 -19.5847 REMARK 3 T TENSOR REMARK 3 T11: 0.1354 T22: 0.1282 REMARK 3 T33: 0.1356 T12: -0.0071 REMARK 3 T13: -0.0097 T23: -0.0019 REMARK 3 L TENSOR REMARK 3 L11: 0.1684 L22: 0.4332 REMARK 3 L33: 0.7006 L12: -0.2864 REMARK 3 L13: -0.2181 L23: -0.6402 REMARK 3 S TENSOR REMARK 3 S11: 0.0129 S12: 0.0230 S13: -0.0516 REMARK 3 S21: 0.0373 S22: 0.0456 S23: 0.0298 REMARK 3 S31: -0.0416 S32: -0.0341 S33: 0.0007 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 6F4T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1200007743. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 75316 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.220 REMARK 200 RESOLUTION RANGE LOW (A) : 50.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.22 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.03600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 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: 6F4R REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PH 6.5, 17.1 % PEG3350, REMARK 280 0.002 M MNCL2, 300 NL SITTING DROPS (SAMPLE:WELL, 1:1 RATIO), REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 24.56850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.22300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.58450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.22300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.56850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.58450 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 HIS A 162 REMARK 465 HIS A 163 REMARK 465 HIS A 164 REMARK 465 HIS A 165 REMARK 465 HIS A 166 REMARK 465 HIS A 167 REMARK 465 SER A 168 REMARK 465 SER A 169 REMARK 465 GLY A 170 REMARK 465 VAL A 171 REMARK 465 ASP A 172 REMARK 465 LEU A 173 REMARK 465 GLY A 174 REMARK 465 THR A 175 REMARK 465 GLU A 176 REMARK 465 ASN A 177 REMARK 465 LEU A 178 REMARK 465 TYR A 179 REMARK 465 PHE A 180 REMARK 465 GLN A 181 REMARK 465 ALA B 142 REMARK 465 TYR B 143 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 GLN A 219 CD OE1 NE2 REMARK 470 GLU A 247 CG CD OE1 OE2 REMARK 470 GLU A 304 CD OE1 OE2 REMARK 470 ASP A 353 OD1 OD2 REMARK 470 LYS A 378 CG CD CE NZ 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 H11 TRS A 506 O HOH A 633 4454 1.50 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 189 60.71 39.27 REMARK 500 ARG A 189 63.50 34.75 REMARK 500 PHE A 199 -53.91 -132.00 REMARK 500 GLU A 266 101.27 -39.52 REMARK 500 ASN A 367 66.45 -151.88 REMARK 500 LYS A 397 -0.18 72.43 REMARK 500 REMARK 500 REMARK: NULL 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 MN A 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 321 NE2 REMARK 620 2 ASP A 323 OD2 107.1 REMARK 620 3 HIS A 400 NE2 84.7 85.8 REMARK 620 4 OGA A 502 O1 161.3 91.3 99.9 REMARK 620 5 OGA A 502 O2' 86.8 165.7 92.8 74.9 REMARK 620 6 HOH B 201 O 85.7 85.5 164.6 93.0 98.6 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 MN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OGA A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRS A 506 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6F4M RELATED DB: PDB REMARK 900 RELATED ID: 6F4N RELATED DB: PDB REMARK 900 RELATED ID: 6F4O RELATED DB: PDB REMARK 900 RELATED ID: 6F4P RELATED DB: PDB REMARK 900 RELATED ID: 6F4Q RELATED DB: PDB REMARK 900 RELATED ID: 6F4R RELATED DB: PDB REMARK 900 RELATED ID: 6F4S RELATED DB: PDB DBREF 6F4T A 183 416 UNP Q8N371 KDM8_HUMAN 183 416 DBREF 6F4T B 139 143 UNP A6NED2 RCCD1_HUMAN 139 143 SEQADV 6F4T HIS A 162 UNP Q8N371 EXPRESSION TAG SEQADV 6F4T HIS A 163 UNP Q8N371 EXPRESSION TAG SEQADV 6F4T HIS A 164 UNP Q8N371 EXPRESSION TAG SEQADV 6F4T HIS A 165 UNP Q8N371 EXPRESSION TAG SEQADV 6F4T HIS A 166 UNP Q8N371 EXPRESSION TAG SEQADV 6F4T HIS A 167 UNP Q8N371 EXPRESSION TAG SEQADV 6F4T SER A 168 UNP Q8N371 EXPRESSION TAG SEQADV 6F4T SER A 169 UNP Q8N371 EXPRESSION TAG SEQADV 6F4T GLY A 170 UNP Q8N371 EXPRESSION TAG SEQADV 6F4T VAL A 171 UNP Q8N371 EXPRESSION TAG SEQADV 6F4T ASP A 172 UNP Q8N371 EXPRESSION TAG SEQADV 6F4T LEU A 173 UNP Q8N371 EXPRESSION TAG SEQADV 6F4T GLY A 174 UNP Q8N371 EXPRESSION TAG SEQADV 6F4T THR A 175 UNP Q8N371 EXPRESSION TAG SEQADV 6F4T GLU A 176 UNP Q8N371 EXPRESSION TAG SEQADV 6F4T ASN A 177 UNP Q8N371 EXPRESSION TAG SEQADV 6F4T LEU A 178 UNP Q8N371 EXPRESSION TAG SEQADV 6F4T TYR A 179 UNP Q8N371 EXPRESSION TAG SEQADV 6F4T PHE A 180 UNP Q8N371 EXPRESSION TAG SEQADV 6F4T GLN A 181 UNP Q8N371 EXPRESSION TAG SEQADV 6F4T SER A 182 UNP Q8N371 EXPRESSION TAG SEQADV 6F4T ALA A 217 UNP Q8N371 CYS 217 ENGINEERED MUTATION SEQADV 6F4T ALA A 232 UNP Q8N371 CYS 232 ENGINEERED MUTATION SEQADV 6F4T CSO A 414 UNP Q8N371 TRP 414 ENGINEERED MUTATION SEQRES 1 A 255 HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU GLY SEQRES 2 A 255 THR GLU ASN LEU TYR PHE GLN SER THR VAL PRO ARG LEU SEQRES 3 A 255 HIS ARG PRO SER LEU GLN HIS PHE ARG GLU GLN PHE LEU SEQRES 4 A 255 VAL PRO GLY ARG PRO VAL ILE LEU LYS GLY VAL ALA ASP SEQRES 5 A 255 HIS TRP PRO ALA MET GLN LYS TRP SER LEU GLU TYR ILE SEQRES 6 A 255 GLN GLU ILE ALA GLY ALA ARG THR VAL PRO VAL GLU VAL SEQRES 7 A 255 GLY SER ARG TYR THR ASP GLU GLU TRP SER GLN THR LEU SEQRES 8 A 255 MET THR VAL ASN GLU PHE ILE SER LYS TYR ILE VAL ASN SEQRES 9 A 255 GLU PRO ARG ASP VAL GLY TYR LEU ALA GLN HIS GLN LEU SEQRES 10 A 255 PHE ASP GLN ILE PRO GLU LEU LYS GLN ASP ILE SER ILE SEQRES 11 A 255 PRO ASP TYR CYS SER LEU GLY ASP GLY GLU GLU GLU GLU SEQRES 12 A 255 ILE THR ILE ASN ALA TRP PHE GLY PRO GLN GLY THR ILE SEQRES 13 A 255 SER PRO LEU HIS GLN ASP PRO GLN GLN ASN PHE LEU VAL SEQRES 14 A 255 GLN VAL MET GLY ARG LYS TYR ILE ARG LEU TYR SER PRO SEQRES 15 A 255 GLN GLU SER GLY ALA LEU TYR PRO HIS ASP THR HIS LEU SEQRES 16 A 255 LEU HIS ASN THR SER GLN VAL ASP VAL GLU ASN PRO ASP SEQRES 17 A 255 LEU GLU LYS PHE PRO LYS PHE ALA LYS ALA PRO PHE LEU SEQRES 18 A 255 SER CYS ILE LEU SER PRO GLY GLU ILE LEU PHE ILE PRO SEQRES 19 A 255 VAL LYS TYR TRP HIS TYR VAL ARG ALA LEU ASP LEU SER SEQRES 20 A 255 PHE SER VAL SER PHE CSO TRP SER SEQRES 1 B 5 CYS ALA ARG ALA TYR HET CSO A 414 19 HET MN A 501 1 HET OGA A 502 13 HET GOL A 503 14 HET GOL A 504 14 HET GOL A 505 14 HET TRS A 506 20 HETNAM CSO S-HYDROXYCYSTEINE HETNAM MN MANGANESE (II) ION HETNAM OGA N-OXALYLGLYCINE HETNAM GOL GLYCEROL HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN TRS TRIS BUFFER FORMUL 1 CSO C3 H7 N O3 S FORMUL 3 MN MN 2+ FORMUL 4 OGA C4 H5 N O5 FORMUL 5 GOL 3(C3 H8 O3) FORMUL 8 TRS C4 H12 N O3 1+ FORMUL 9 HOH *338(H2 O) HELIX 1 AA1 SER A 191 PHE A 199 1 9 HELIX 2 AA2 VAL A 211 HIS A 214 5 4 HELIX 3 AA3 TRP A 215 TRP A 221 1 7 HELIX 4 AA4 SER A 222 GLY A 231 1 10 HELIX 5 AA5 VAL A 255 ILE A 263 1 9 HELIX 6 AA6 GLN A 277 ILE A 282 1 6 HELIX 7 AA7 ILE A 282 GLN A 287 1 6 HELIX 8 AA8 PRO A 292 GLY A 298 5 7 HELIX 9 AA9 GLU A 301 ILE A 305 5 5 HELIX 10 AB1 SER A 342 LEU A 349 5 8 HELIX 11 AB2 PHE A 373 ALA A 379 5 7 SHEET 1 AA1 9 ARG A 186 HIS A 188 0 SHEET 2 AA1 9 VAL A 206 LYS A 209 1 O LYS A 209 N LEU A 187 SHEET 3 AA1 9 ILE A 391 ILE A 394 -1 O PHE A 393 N VAL A 206 SHEET 4 AA1 9 GLN A 326 MET A 333 -1 N LEU A 329 O LEU A 392 SHEET 5 AA1 9 SER A 408 TRP A 415 -1 O VAL A 411 N VAL A 330 SHEET 6 AA1 9 THR A 306 GLY A 312 -1 N GLY A 312 O SER A 408 SHEET 7 AA1 9 GLY A 271 HIS A 276 -1 N HIS A 276 O ALA A 309 SHEET 8 AA1 9 THR A 234 VAL A 239 -1 N GLU A 238 O TYR A 272 SHEET 9 AA1 9 SER A 249 THR A 254 -1 O SER A 249 N VAL A 239 SHEET 1 AA2 4 ILE A 317 HIS A 321 0 SHEET 2 AA2 4 TRP A 399 ALA A 404 -1 O HIS A 400 N HIS A 321 SHEET 3 AA2 4 LYS A 336 TYR A 341 -1 N TYR A 337 O ARG A 403 SHEET 4 AA2 4 LEU A 382 LEU A 386 -1 O LEU A 386 N LYS A 336 SSBOND 1 CSO A 414 CYS B 139 1555 1555 2.16 LINK C PHE A 413 N ACSO A 414 1555 1555 1.34 LINK C PHE A 413 N BCSO A 414 1555 1555 1.33 LINK C ACSO A 414 N TRP A 415 1555 1555 1.33 LINK C BCSO A 414 N TRP A 415 1555 1555 1.29 LINK NE2 HIS A 321 MN MN A 501 1555 1555 2.22 LINK OD2 ASP A 323 MN MN A 501 1555 1555 2.14 LINK NE2 HIS A 400 MN MN A 501 1555 1555 2.27 LINK MN MN A 501 O1 OGA A 502 1555 1555 2.17 LINK MN MN A 501 O2' OGA A 502 1555 1555 2.19 LINK MN MN A 501 O HOH B 201 1555 1555 2.26 SITE 1 AC1 5 HIS A 321 ASP A 323 HIS A 400 OGA A 502 SITE 2 AC1 5 HOH B 201 SITE 1 AC2 14 TYR A 272 TRP A 310 SER A 318 HIS A 321 SITE 2 AC2 14 ASP A 323 ASN A 327 LEU A 329 LYS A 336 SITE 3 AC2 14 HIS A 400 VAL A 402 SER A 412 MN A 501 SITE 4 AC2 14 HOH A 728 CYS B 139 SITE 1 AC3 7 ARG A 189 GLU A 266 ASP A 293 TYR A 294 SITE 2 AC3 7 HOH A 630 HOH A 708 HOH A 755 SITE 1 AC4 6 GLN A 250 LEU A 252 ARG A 335 HOH A 605 SITE 2 AC4 6 HOH A 632 HOH A 772 SITE 1 AC5 3 GLU A 257 SER A 260 HOH A 609 SITE 1 AC6 13 LEU A 200 VAL A 201 GLY A 203 GLN A 326 SITE 2 AC6 13 TYR A 350 LYS A 372 PHE A 373 VAL A 396 SITE 3 AC6 13 HOH A 603 HOH A 612 HOH A 633 HOH A 669 SITE 4 AC6 13 HOH A 689 CRYST1 49.137 65.169 78.446 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 0.020351 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015345 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012748 0.00000