HEADER OXIDOREDUCTASE 30-NOV-17 6F4S TITLE HUMAN JMJD5 (N308C) IN COMPLEX WITH MN(II), 2OG AND RCCD1 (139-143) TITLE 2 (COMPLEX-4) COMPND MOL_ID: 1; COMPND 2 MOLECULE: JMJC DOMAIN-CONTAINING PROTEIN 5; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LYSINE-SPECIFIC DEMETHYLASE 8, JUMONJI DOMAIN-CONTAINING COMPND 5 PROTEIN 5; COMPND 6 EC: 1.14.11.47; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 OTHER_DETAILS: CATALYTIC DOMAIN FRAGMENT: 183-416; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: RCC1 DOMAIN-CONTAINING PROTEIN 1; COMPND 12 CHAIN: B; COMPND 13 ENGINEERED: YES; COMPND 14 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 3 23-OCT-24 6F4S 1 REMARK REVDAT 2 17-JAN-24 6F4S 1 LINK REVDAT 1 04-APR-18 6F4S 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. 1.46 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) : 1.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 44307 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.138 REMARK 3 R VALUE (WORKING SET) : 0.137 REMARK 3 FREE R VALUE : 0.152 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 2188 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 33.4345 - 3.6808 0.99 2819 140 0.1501 0.1453 REMARK 3 2 3.6808 - 2.9221 1.00 2692 146 0.1196 0.1372 REMARK 3 3 2.9221 - 2.5529 1.00 2669 137 0.1228 0.1563 REMARK 3 4 2.5529 - 2.3195 1.00 2648 138 0.1155 0.1414 REMARK 3 5 2.3195 - 2.1533 1.00 2644 137 0.1093 0.1196 REMARK 3 6 2.1533 - 2.0264 1.00 2640 141 0.1138 0.1354 REMARK 3 7 2.0264 - 1.9249 1.00 2630 119 0.1174 0.1387 REMARK 3 8 1.9249 - 1.8411 1.00 2610 132 0.1315 0.1338 REMARK 3 9 1.8411 - 1.7702 1.00 2615 135 0.1354 0.1716 REMARK 3 10 1.7702 - 1.7091 1.00 2611 143 0.1447 0.1695 REMARK 3 11 1.7091 - 1.6557 1.00 2599 145 0.1590 0.1703 REMARK 3 12 1.6557 - 1.6084 1.00 2595 130 0.1693 0.2066 REMARK 3 13 1.6084 - 1.5660 1.00 2595 160 0.1818 0.2042 REMARK 3 14 1.5660 - 1.5278 1.00 2562 138 0.2007 0.2312 REMARK 3 15 1.5278 - 1.4931 1.00 2618 101 0.2103 0.1986 REMARK 3 16 1.4931 - 1.4613 0.99 2572 146 0.2318 0.2262 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 : 62.40 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.600 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.75000 REMARK 3 B22 (A**2) : 0.34000 REMARK 3 B33 (A**2) : 2.41000 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 : 0.008 2440 REMARK 3 ANGLE : 0.962 3364 REMARK 3 CHIRALITY : 0.085 336 REMARK 3 PLANARITY : 0.007 462 REMARK 3 DIHEDRAL : 15.403 934 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): -25.0410 22.3715 -19.5715 REMARK 3 T TENSOR REMARK 3 T11: 0.1165 T22: 0.1751 REMARK 3 T33: 0.1884 T12: 0.0541 REMARK 3 T13: 0.0295 T23: 0.0362 REMARK 3 L TENSOR REMARK 3 L11: 0.8805 L22: 1.5717 REMARK 3 L33: 1.5703 L12: -0.1679 REMARK 3 L13: -0.4990 L23: 0.5488 REMARK 3 S TENSOR REMARK 3 S11: 0.0057 S12: 0.0162 S13: 0.2286 REMARK 3 S21: 0.0730 S22: 0.0854 S23: 0.2724 REMARK 3 S31: -0.2935 S32: -0.3660 S33: 0.0791 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 212:230) REMARK 3 ORIGIN FOR THE GROUP (A): -8.2726 10.3833 -2.6835 REMARK 3 T TENSOR REMARK 3 T11: 0.2518 T22: 0.2076 REMARK 3 T33: 0.1422 T12: 0.0309 REMARK 3 T13: 0.0114 T23: -0.0276 REMARK 3 L TENSOR REMARK 3 L11: 2.4875 L22: 1.9717 REMARK 3 L33: 1.9064 L12: -0.7527 REMARK 3 L13: 0.8087 L23: -0.4890 REMARK 3 S TENSOR REMARK 3 S11: -0.1584 S12: -0.3354 S13: 0.2661 REMARK 3 S21: 0.3988 S22: 0.1991 S23: -0.1509 REMARK 3 S31: -0.3153 S32: -0.0445 S33: 0.0068 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 231:254) REMARK 3 ORIGIN FOR THE GROUP (A): 3.2903 4.4737 -22.1839 REMARK 3 T TENSOR REMARK 3 T11: 0.1702 T22: 0.1779 REMARK 3 T33: 0.1581 T12: 0.0281 REMARK 3 T13: 0.0313 T23: 0.0216 REMARK 3 L TENSOR REMARK 3 L11: 0.9336 L22: 2.0521 REMARK 3 L33: 1.4848 L12: -0.6296 REMARK 3 L13: 0.5435 L23: -1.1312 REMARK 3 S TENSOR REMARK 3 S11: 0.0960 S12: 0.2383 S13: 0.0492 REMARK 3 S21: -0.2901 S22: -0.1876 S23: -0.1440 REMARK 3 S31: 0.1136 S32: 0.2112 S33: 0.0550 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 255:277) REMARK 3 ORIGIN FOR THE GROUP (A): 5.7779 7.7153 -14.4776 REMARK 3 T TENSOR REMARK 3 T11: 0.0997 T22: 0.1439 REMARK 3 T33: 0.1767 T12: -0.0088 REMARK 3 T13: 0.0046 T23: 0.0225 REMARK 3 L TENSOR REMARK 3 L11: 1.3081 L22: 2.3911 REMARK 3 L33: 1.8329 L12: -0.3872 REMARK 3 L13: 0.1200 L23: -0.6392 REMARK 3 S TENSOR REMARK 3 S11: 0.0281 S12: 0.0733 S13: 0.0803 REMARK 3 S21: 0.0678 S22: -0.1200 S23: -0.4189 REMARK 3 S31: -0.0434 S32: 0.3691 S33: -0.0283 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 278:305) REMARK 3 ORIGIN FOR THE GROUP (A): -19.9586 3.8374 -13.7133 REMARK 3 T TENSOR REMARK 3 T11: 0.1648 T22: 0.1774 REMARK 3 T33: 0.2329 T12: -0.0238 REMARK 3 T13: 0.0164 T23: 0.0307 REMARK 3 L TENSOR REMARK 3 L11: 2.0950 L22: 1.7649 REMARK 3 L33: 0.6690 L12: -0.8476 REMARK 3 L13: 0.0858 L23: -0.6492 REMARK 3 S TENSOR REMARK 3 S11: -0.0477 S12: -0.0115 S13: -0.5431 REMARK 3 S21: 0.0130 S22: 0.1242 S23: 0.3967 REMARK 3 S31: 0.1285 S32: -0.2378 S33: -0.0851 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 306:312) REMARK 3 ORIGIN FOR THE GROUP (A): -8.4578 7.5100 -16.5127 REMARK 3 T TENSOR REMARK 3 T11: 0.1051 T22: 0.0914 REMARK 3 T33: 0.1172 T12: 0.0065 REMARK 3 T13: -0.0018 T23: -0.0054 REMARK 3 L TENSOR REMARK 3 L11: 3.0479 L22: 1.9183 REMARK 3 L33: 1.0875 L12: 0.5257 REMARK 3 L13: 0.1069 L23: -0.0354 REMARK 3 S TENSOR REMARK 3 S11: -0.0342 S12: 0.1138 S13: -0.1907 REMARK 3 S21: -0.0434 S22: 0.0968 S23: 0.0822 REMARK 3 S31: 0.0196 S32: -0.0134 S33: 0.0134 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 313:325) REMARK 3 ORIGIN FOR THE GROUP (A): -6.3590 13.4274 -25.5823 REMARK 3 T TENSOR REMARK 3 T11: 0.0953 T22: 0.0826 REMARK 3 T33: 0.0918 T12: 0.0013 REMARK 3 T13: -0.0059 T23: -0.0113 REMARK 3 L TENSOR REMARK 3 L11: 1.5806 L22: 0.8350 REMARK 3 L33: 1.7468 L12: -0.2572 REMARK 3 L13: 0.2556 L23: -0.5826 REMARK 3 S TENSOR REMARK 3 S11: 0.0028 S12: 0.1450 S13: -0.0966 REMARK 3 S21: 0.0134 S22: 0.0299 S23: -0.0832 REMARK 3 S31: 0.0208 S32: 0.1125 S33: 0.0342 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 326:341) REMARK 3 ORIGIN FOR THE GROUP (A): -10.0386 18.7642 -19.7509 REMARK 3 T TENSOR REMARK 3 T11: 0.0970 T22: 0.0866 REMARK 3 T33: 0.0900 T12: 0.0094 REMARK 3 T13: 0.0051 T23: -0.0075 REMARK 3 L TENSOR REMARK 3 L11: 0.7088 L22: 1.0594 REMARK 3 L33: 1.5248 L12: 0.0398 REMARK 3 L13: -0.0355 L23: -0.6116 REMARK 3 S TENSOR REMARK 3 S11: 0.0079 S12: -0.0486 S13: 0.0053 REMARK 3 S21: 0.1089 S22: 0.0257 S23: 0.0283 REMARK 3 S31: -0.0998 S32: -0.0025 S33: 0.0350 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN A AND RESID 342:365) REMARK 3 ORIGIN FOR THE GROUP (A): -8.0131 15.1023 -37.4026 REMARK 3 T TENSOR REMARK 3 T11: 0.1771 T22: 0.1418 REMARK 3 T33: 0.1278 T12: -0.0147 REMARK 3 T13: 0.0034 T23: -0.0288 REMARK 3 L TENSOR REMARK 3 L11: 1.9089 L22: 2.1523 REMARK 3 L33: 2.3267 L12: 0.0441 REMARK 3 L13: -0.6613 L23: -0.6414 REMARK 3 S TENSOR REMARK 3 S11: -0.0492 S12: 0.2676 S13: -0.3192 REMARK 3 S21: -0.2968 S22: -0.0223 S23: 0.0566 REMARK 3 S31: 0.2941 S32: -0.0827 S33: -0.0032 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN A AND RESID 366:381) REMARK 3 ORIGIN FOR THE GROUP (A): -2.1511 24.8335 -38.8253 REMARK 3 T TENSOR REMARK 3 T11: 0.1716 T22: 0.1532 REMARK 3 T33: 0.1209 T12: 0.0008 REMARK 3 T13: 0.0404 T23: 0.0107 REMARK 3 L TENSOR REMARK 3 L11: 0.7443 L22: 1.3721 REMARK 3 L33: 2.5058 L12: -0.2480 REMARK 3 L13: -1.0756 L23: 0.8909 REMARK 3 S TENSOR REMARK 3 S11: 0.1739 S12: 0.2744 S13: 0.0594 REMARK 3 S21: -0.1631 S22: -0.0404 S23: -0.1130 REMARK 3 S31: -0.2554 S32: 0.0575 S33: -0.0232 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN A AND RESID 382:399) REMARK 3 ORIGIN FOR THE GROUP (A): -14.4944 19.2960 -22.7439 REMARK 3 T TENSOR REMARK 3 T11: 0.0929 T22: 0.0865 REMARK 3 T33: 0.1042 T12: 0.0263 REMARK 3 T13: 0.0034 T23: 0.0001 REMARK 3 L TENSOR REMARK 3 L11: 1.2548 L22: 1.2695 REMARK 3 L33: 1.5348 L12: 0.2350 REMARK 3 L13: -0.2907 L23: -0.4670 REMARK 3 S TENSOR REMARK 3 S11: 0.0025 S12: -0.0002 S13: 0.0730 REMARK 3 S21: 0.0569 S22: 0.0568 S23: 0.1055 REMARK 3 S31: -0.1249 S32: -0.0911 S33: 0.0124 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: (CHAIN A AND RESID 400:416) REMARK 3 ORIGIN FOR THE GROUP (A): -10.7116 13.0317 -19.6228 REMARK 3 T TENSOR REMARK 3 T11: 0.1007 T22: 0.0845 REMARK 3 T33: 0.0943 T12: 0.0082 REMARK 3 T13: -0.0073 T23: -0.0089 REMARK 3 L TENSOR REMARK 3 L11: 0.7420 L22: 1.0999 REMARK 3 L33: 1.7250 L12: -0.1589 REMARK 3 L13: -0.4900 L23: -1.0861 REMARK 3 S TENSOR REMARK 3 S11: -0.0091 S12: 0.0447 S13: -0.0714 REMARK 3 S21: 0.0362 S22: 0.0521 S23: 0.0215 REMARK 3 S31: 0.0333 S32: -0.0666 S33: 0.0222 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 6F4S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1200007742. 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 : HKL-2000 706E REMARK 200 DATA SCALING SOFTWARE : HKL-2000 706E REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44375 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.460 REMARK 200 RESOLUTION RANGE LOW (A) : 33.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.11300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.46 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 1.30000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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 (%): 45.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PH 6.5, 29 % PEG3350, REMARK 280 0.002 M MNCL2, 300 NL SITTING DROPS (SAMPLE:WELL, 1:2 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 24.66050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.84550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.80350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.84550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.66050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.80350 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 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 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 GLU A 247 CG CD OE1 OE2 REMARK 470 ASP A 353 CG OD1 OD2 REMARK 470 LYS A 378 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 HIS A 355 HD1 HIS A 358 1.58 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 61.59 38.18 REMARK 500 PHE A 199 -51.71 -130.77 REMARK 500 GLU A 266 99.30 -45.58 REMARK 500 ASN A 367 67.76 -152.25 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 936 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A 937 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH A 938 DISTANCE = 6.71 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 MN A 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 321 NE2 REMARK 620 2 ASP A 323 OD2 109.6 REMARK 620 3 HIS A 400 NE2 83.7 85.1 REMARK 620 4 AKG A 502 O5 86.5 162.8 90.8 REMARK 620 5 AKG A 502 O1 160.8 89.2 102.3 75.4 REMARK 620 6 HOH A 755 O 85.5 88.8 165.1 98.8 91.2 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 AKG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRS 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 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: 6F4T RELATED DB: PDB DBREF 6F4S A 183 416 UNP Q8N371 KDM8_HUMAN 183 416 DBREF 6F4S B 139 143 UNP A6NED2 RCCD1_HUMAN 139 143 SEQADV 6F4S HIS A 162 UNP Q8N371 EXPRESSION TAG SEQADV 6F4S HIS A 163 UNP Q8N371 EXPRESSION TAG SEQADV 6F4S HIS A 164 UNP Q8N371 EXPRESSION TAG SEQADV 6F4S HIS A 165 UNP Q8N371 EXPRESSION TAG SEQADV 6F4S HIS A 166 UNP Q8N371 EXPRESSION TAG SEQADV 6F4S HIS A 167 UNP Q8N371 EXPRESSION TAG SEQADV 6F4S SER A 168 UNP Q8N371 EXPRESSION TAG SEQADV 6F4S SER A 169 UNP Q8N371 EXPRESSION TAG SEQADV 6F4S GLY A 170 UNP Q8N371 EXPRESSION TAG SEQADV 6F4S VAL A 171 UNP Q8N371 EXPRESSION TAG SEQADV 6F4S ASP A 172 UNP Q8N371 EXPRESSION TAG SEQADV 6F4S LEU A 173 UNP Q8N371 EXPRESSION TAG SEQADV 6F4S GLY A 174 UNP Q8N371 EXPRESSION TAG SEQADV 6F4S THR A 175 UNP Q8N371 EXPRESSION TAG SEQADV 6F4S GLU A 176 UNP Q8N371 EXPRESSION TAG SEQADV 6F4S ASN A 177 UNP Q8N371 EXPRESSION TAG SEQADV 6F4S LEU A 178 UNP Q8N371 EXPRESSION TAG SEQADV 6F4S TYR A 179 UNP Q8N371 EXPRESSION TAG SEQADV 6F4S PHE A 180 UNP Q8N371 EXPRESSION TAG SEQADV 6F4S GLN A 181 UNP Q8N371 EXPRESSION TAG SEQADV 6F4S SER A 182 UNP Q8N371 EXPRESSION TAG SEQADV 6F4S ALA A 217 UNP Q8N371 CYS 217 ENGINEERED MUTATION SEQADV 6F4S ALA A 232 UNP Q8N371 CYS 232 ENGINEERED MUTATION SEQADV 6F4S CYS A 308 UNP Q8N371 ASN 308 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 CYS 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 TRP TRP SER SEQRES 1 B 5 CYS ALA ARG ALA TYR HET MN A 501 1 HET AKG A 502 14 HET TRS A 503 20 HET GOL A 504 14 HETNAM MN MANGANESE (II) ION HETNAM AKG 2-OXOGLUTARIC ACID HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM GOL GLYCEROL HETSYN TRS TRIS BUFFER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 MN MN 2+ FORMUL 4 AKG C5 H6 O5 FORMUL 5 TRS C4 H12 N O3 1+ FORMUL 6 GOL C3 H8 O3 FORMUL 7 HOH *342(H2 O) HELIX 1 AA1 SER A 191 PHE A 199 1 9 HELIX 2 AA2 PRO A 216 TRP A 221 1 6 HELIX 3 AA3 SER A 222 GLY A 231 1 10 HELIX 4 AA4 VAL A 255 ILE A 263 1 9 HELIX 5 AA5 GLN A 277 ILE A 282 1 6 HELIX 6 AA6 ILE A 282 GLN A 287 1 6 HELIX 7 AA7 PRO A 292 GLY A 298 5 7 HELIX 8 AA8 GLU A 301 ILE A 305 5 5 HELIX 9 AA9 SER A 342 TYR A 350 5 9 HELIX 10 AB1 THR A 354 HIS A 358 5 5 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 382 N LEU A 340 SSBOND 1 CYS A 308 CYS B 139 1555 1555 1.99 LINK NE2 HIS A 321 MN MN A 501 1555 1555 2.21 LINK OD2 ASP A 323 MN MN A 501 1555 1555 2.10 LINK NE2 HIS A 400 MN MN A 501 1555 1555 2.27 LINK MN MN A 501 O5 AKG A 502 1555 1555 2.22 LINK MN MN A 501 O1 AKG A 502 1555 1555 2.20 LINK MN MN A 501 O HOH A 755 1555 1555 2.25 SITE 1 AC1 5 HIS A 321 ASP A 323 HIS A 400 AKG A 502 SITE 2 AC1 5 HOH A 755 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 TRP A 414 SITE 4 AC2 14 MN A 501 HOH A 743 SITE 1 AC3 13 LEU A 200 VAL A 201 GLY A 203 GLN A 326 SITE 2 AC3 13 TYR A 350 LYS A 372 PHE A 373 VAL A 396 SITE 3 AC3 13 HOH A 602 HOH A 615 HOH A 673 HOH A 681 SITE 4 AC3 13 HOH A 740 SITE 1 AC4 7 PRO A 190 GLU A 266 ASP A 293 TYR A 294 SITE 2 AC4 7 HOH A 670 HOH A 676 HOH A 699 CRYST1 49.321 65.607 77.691 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 0.020275 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015242 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012872 0.00000