HEADER OXIDOREDUCTASE 29-NOV-17 6F4P TITLE HUMAN JMJD5 IN COMPLEX WITH MN, NOG AND RPS6 (129-144) (COMPLEX-1) 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 OTHER_DETAILS: FRAGMENT: 183-416; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: 40S RIBOSOMAL PROTEIN S6; COMPND 12 CHAIN: B; COMPND 13 FRAGMENT: UNP RESIDUES 129-144; COMPND 14 SYNONYM: PHOSPHOPROTEIN NP33,SMALL RIBOSOMAL SUBUNIT PROTEIN ES6; COMPND 15 ENGINEERED: YES; COMPND 16 OTHER_DETAILS: FRAGMENT: 129-144 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 6F4P 1 LINK REVDAT 1 04-APR-18 6F4P 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. 1.45 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 44577 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.168 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860 REMARK 3 FREE R VALUE TEST SET COUNT : 2165 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 32.4706 - 3.5746 1.00 3046 156 0.1549 0.1838 REMARK 3 2 3.5746 - 2.8378 1.00 2910 157 0.1281 0.1335 REMARK 3 3 2.8378 - 2.4792 1.00 2864 160 0.1320 0.1388 REMARK 3 4 2.4792 - 2.2526 1.00 2867 142 0.1263 0.1700 REMARK 3 5 2.2526 - 2.0912 0.99 2875 125 0.1274 0.1432 REMARK 3 6 2.0912 - 1.9679 0.99 2824 143 0.1188 0.1522 REMARK 3 7 1.9679 - 1.8694 0.99 2828 153 0.1326 0.1569 REMARK 3 8 1.8694 - 1.7880 0.99 2810 138 0.1426 0.1558 REMARK 3 9 1.7880 - 1.7192 0.99 2807 142 0.1517 0.1842 REMARK 3 10 1.7192 - 1.6598 0.99 2764 151 0.1673 0.1924 REMARK 3 11 1.6598 - 1.6080 0.98 2815 122 0.1742 0.1925 REMARK 3 12 1.6080 - 1.5620 0.98 2773 128 0.1967 0.2376 REMARK 3 13 1.5620 - 1.5209 0.98 2766 152 0.2188 0.2714 REMARK 3 14 1.5209 - 1.4838 0.98 2735 147 0.2395 0.2564 REMARK 3 15 1.4838 - 1.4500 0.98 2728 149 0.2772 0.2766 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 : 60.30 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.850 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.11000 REMARK 3 B22 (A**2) : -0.23000 REMARK 3 B33 (A**2) : 3.34000 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 : 0.009 2299 REMARK 3 ANGLE : 1.005 3169 REMARK 3 CHIRALITY : 0.087 324 REMARK 3 PLANARITY : 0.008 428 REMARK 3 DIHEDRAL : 13.552 860 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): -24.8504 22.4529 -20.6559 REMARK 3 T TENSOR REMARK 3 T11: 0.1644 T22: 0.2546 REMARK 3 T33: 0.2274 T12: 0.0678 REMARK 3 T13: 0.0333 T23: 0.0353 REMARK 3 L TENSOR REMARK 3 L11: 0.6490 L22: 0.5881 REMARK 3 L33: 0.6781 L12: -0.3896 REMARK 3 L13: -0.0754 L23: -0.1786 REMARK 3 S TENSOR REMARK 3 S11: -0.0281 S12: -0.0555 S13: 0.2142 REMARK 3 S21: 0.0535 S22: 0.1128 S23: 0.2294 REMARK 3 S31: -0.2799 S32: -0.3623 S33: 0.0864 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 212:230) REMARK 3 ORIGIN FOR THE GROUP (A): -8.4368 10.4684 -3.2697 REMARK 3 T TENSOR REMARK 3 T11: 0.2818 T22: 0.2658 REMARK 3 T33: 0.1840 T12: 0.0522 REMARK 3 T13: 0.0080 T23: -0.0184 REMARK 3 L TENSOR REMARK 3 L11: 0.2168 L22: 0.2144 REMARK 3 L33: 0.7011 L12: 0.2029 REMARK 3 L13: 0.0980 L23: 0.1067 REMARK 3 S TENSOR REMARK 3 S11: -0.1366 S12: -0.1802 S13: 0.0650 REMARK 3 S21: 0.3526 S22: 0.2047 S23: -0.0526 REMARK 3 S31: -0.1163 S32: -0.0495 S33: 0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 231:254) REMARK 3 ORIGIN FOR THE GROUP (A): 2.9637 4.2589 -21.4240 REMARK 3 T TENSOR REMARK 3 T11: 0.2125 T22: 0.2010 REMARK 3 T33: 0.2179 T12: 0.0382 REMARK 3 T13: 0.0346 T23: 0.0488 REMARK 3 L TENSOR REMARK 3 L11: 0.8449 L22: 0.7242 REMARK 3 L33: 0.3825 L12: -0.3703 REMARK 3 L13: 0.2240 L23: 0.3917 REMARK 3 S TENSOR REMARK 3 S11: 0.0738 S12: 0.2596 S13: 0.0536 REMARK 3 S21: -0.2634 S22: -0.1427 S23: -0.1169 REMARK 3 S31: 0.0471 S32: 0.0901 S33: 0.0001 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 255:277) REMARK 3 ORIGIN FOR THE GROUP (A): 5.0420 7.8287 -13.9283 REMARK 3 T TENSOR REMARK 3 T11: 0.1360 T22: 0.1363 REMARK 3 T33: 0.2161 T12: -0.0070 REMARK 3 T13: -0.0157 T23: 0.0390 REMARK 3 L TENSOR REMARK 3 L11: 0.5405 L22: 1.2747 REMARK 3 L33: 1.1544 L12: -0.9821 REMARK 3 L13: 0.0466 L23: -0.6888 REMARK 3 S TENSOR REMARK 3 S11: -0.0167 S12: 0.2044 S13: 0.0293 REMARK 3 S21: 0.0487 S22: -0.1099 S23: -0.3024 REMARK 3 S31: 0.0234 S32: 0.2346 S33: -0.0412 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 278:305) REMARK 3 ORIGIN FOR THE GROUP (A): -19.2095 4.6584 -12.7545 REMARK 3 T TENSOR REMARK 3 T11: 0.2144 T22: 0.2481 REMARK 3 T33: 0.2799 T12: -0.0173 REMARK 3 T13: 0.0170 T23: 0.0474 REMARK 3 L TENSOR REMARK 3 L11: 0.3360 L22: 0.6663 REMARK 3 L33: 0.3198 L12: 0.2840 REMARK 3 L13: -0.3223 L23: -0.6577 REMARK 3 S TENSOR REMARK 3 S11: -0.1195 S12: 0.0260 S13: -0.3595 REMARK 3 S21: 0.0300 S22: 0.0809 S23: 0.2693 REMARK 3 S31: 0.1506 S32: -0.2196 S33: -0.0287 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 306:312) REMARK 3 ORIGIN FOR THE GROUP (A): -8.9071 7.2352 -16.8008 REMARK 3 T TENSOR REMARK 3 T11: 0.1571 T22: 0.1197 REMARK 3 T33: 0.1659 T12: 0.0112 REMARK 3 T13: -0.0192 T23: 0.0043 REMARK 3 L TENSOR REMARK 3 L11: 0.1685 L22: 0.2648 REMARK 3 L33: 0.0901 L12: -0.2996 REMARK 3 L13: -0.1383 L23: 0.1962 REMARK 3 S TENSOR REMARK 3 S11: 0.1275 S12: -0.0098 S13: -0.0048 REMARK 3 S21: 0.0312 S22: 0.0232 S23: 0.1649 REMARK 3 S31: -0.0156 S32: 0.0984 S33: 0.0005 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 313:325) REMARK 3 ORIGIN FOR THE GROUP (A): -6.3978 13.3364 -25.7345 REMARK 3 T TENSOR REMARK 3 T11: 0.1315 T22: 0.1244 REMARK 3 T33: 0.1349 T12: -0.0059 REMARK 3 T13: -0.0159 T23: -0.0065 REMARK 3 L TENSOR REMARK 3 L11: 0.2412 L22: 0.4197 REMARK 3 L33: 0.5723 L12: -0.1028 REMARK 3 L13: -0.3338 L23: -0.1531 REMARK 3 S TENSOR REMARK 3 S11: 0.0384 S12: 0.1470 S13: -0.1013 REMARK 3 S21: -0.0251 S22: 0.0222 S23: -0.0665 REMARK 3 S31: 0.0929 S32: 0.0989 S33: 0.0000 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 326:341) REMARK 3 ORIGIN FOR THE GROUP (A): -9.7440 19.0998 -20.1389 REMARK 3 T TENSOR REMARK 3 T11: 0.1554 T22: 0.1428 REMARK 3 T33: 0.1387 T12: -0.0004 REMARK 3 T13: -0.0061 T23: -0.0030 REMARK 3 L TENSOR REMARK 3 L11: 0.4259 L22: 0.4120 REMARK 3 L33: 0.3059 L12: -0.2724 REMARK 3 L13: -0.0460 L23: -0.1131 REMARK 3 S TENSOR REMARK 3 S11: -0.0038 S12: -0.0775 S13: 0.0154 REMARK 3 S21: 0.0792 S22: 0.0539 S23: 0.0374 REMARK 3 S31: -0.0713 S32: -0.0083 S33: -0.0000 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN A AND RESID 342:365) REMARK 3 ORIGIN FOR THE GROUP (A): -8.0317 14.4035 -37.6983 REMARK 3 T TENSOR REMARK 3 T11: 0.1823 T22: 0.1363 REMARK 3 T33: 0.1123 T12: -0.0167 REMARK 3 T13: 0.0104 T23: -0.0289 REMARK 3 L TENSOR REMARK 3 L11: 0.6809 L22: 0.4851 REMARK 3 L33: 1.1714 L12: 0.0155 REMARK 3 L13: -0.8622 L23: -0.6929 REMARK 3 S TENSOR REMARK 3 S11: -0.0352 S12: 0.2325 S13: -0.1760 REMARK 3 S21: -0.1987 S22: -0.0035 S23: -0.0325 REMARK 3 S31: 0.1719 S32: -0.0361 S33: -0.0001 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN A AND RESID 366:381) REMARK 3 ORIGIN FOR THE GROUP (A): -2.2172 24.6460 -39.1006 REMARK 3 T TENSOR REMARK 3 T11: 0.1972 T22: 0.1879 REMARK 3 T33: 0.1516 T12: 0.0210 REMARK 3 T13: 0.0554 T23: 0.0159 REMARK 3 L TENSOR REMARK 3 L11: 0.2445 L22: 0.4736 REMARK 3 L33: 0.2438 L12: 0.2436 REMARK 3 L13: -0.1301 L23: 0.2932 REMARK 3 S TENSOR REMARK 3 S11: 0.2142 S12: 0.0989 S13: 0.1327 REMARK 3 S21: -0.0126 S22: -0.0060 S23: -0.1104 REMARK 3 S31: -0.3281 S32: 0.0972 S33: 0.0015 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN A AND RESID 382:399) REMARK 3 ORIGIN FOR THE GROUP (A): -14.5610 19.1766 -22.9708 REMARK 3 T TENSOR REMARK 3 T11: 0.1478 T22: 0.1393 REMARK 3 T33: 0.1381 T12: 0.0160 REMARK 3 T13: 0.0028 T23: -0.0025 REMARK 3 L TENSOR REMARK 3 L11: 0.6479 L22: 0.3978 REMARK 3 L33: 0.3120 L12: -0.0195 REMARK 3 L13: -0.1940 L23: -0.4018 REMARK 3 S TENSOR REMARK 3 S11: -0.0163 S12: 0.0435 S13: 0.0531 REMARK 3 S21: 0.0457 S22: 0.0887 S23: 0.1128 REMARK 3 S31: -0.1174 S32: -0.0613 S33: 0.0011 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: (CHAIN A AND RESID 400:416) REMARK 3 ORIGIN FOR THE GROUP (A): -10.7552 13.0232 -19.7345 REMARK 3 T TENSOR REMARK 3 T11: 0.1421 T22: 0.1322 REMARK 3 T33: 0.1362 T12: -0.0053 REMARK 3 T13: -0.0104 T23: -0.0013 REMARK 3 L TENSOR REMARK 3 L11: 0.4876 L22: 0.6424 REMARK 3 L33: 0.7693 L12: -0.3829 REMARK 3 L13: -0.4598 L23: -0.6814 REMARK 3 S TENSOR REMARK 3 S11: -0.0287 S12: 0.0447 S13: -0.0981 REMARK 3 S21: 0.0442 S22: 0.0816 S23: -0.0123 REMARK 3 S31: 0.0092 S32: -0.0405 S33: -0.0000 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 6F4P 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_1200007739. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JAN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 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 : NULL REMARK 200 OPTICS : NULL 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 : 44727 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 32.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 8.40 REMARK 200 R MERGE FOR SHELL (I) : 1.20000 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: 6F4O REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PH 6.0, 26.4 % 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 24.64150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.01850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.46250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.01850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.64150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.46250 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 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 VAL B 135 REMARK 465 PRO B 136 REMARK 465 ARG B 138 REMARK 465 LEU B 139 REMARK 465 GLY B 140 REMARK 465 PRO B 141 REMARK 465 LYS B 142 REMARK 465 ARG B 143 REMARK 465 ALA B 144 REMARK 465 SER B 145 REMARK 465 ARG B 146 REMARK 465 ILE B 147 REMARK 465 ARG B 148 REMARK 465 LYS B 149 REMARK 465 LEU B 150 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 181 CG CD OE1 NE2 REMARK 470 GLN A 219 CD OE1 NE2 REMARK 470 GLU A 246 CG CD OE1 OE2 REMARK 470 GLU A 247 CG CD OE1 OE2 REMARK 470 GLU A 303 CD OE1 OE2 REMARK 470 GLU A 304 CG CD OE1 OE2 REMARK 470 GLN A 344 CD OE1 NE2 REMARK 470 ASP A 353 CG OD1 OD2 REMARK 470 LEU A 356 CG CD1 CD2 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 1.55 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 H12 TRS A 503 O HOH A 677 4454 1.54 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 57.83 38.75 REMARK 500 PHE A 199 -52.24 -128.06 REMARK 500 PHE A 199 -52.24 -132.73 REMARK 500 ILE A 263 -62.23 -121.16 REMARK 500 GLU A 266 98.73 -46.16 REMARK 500 ASN A 367 68.11 -151.40 REMARK 500 LYS A 397 -1.41 72.65 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 928 DISTANCE = 6.02 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 107.8 REMARK 620 3 HIS A 400 NE2 84.5 83.8 REMARK 620 4 OGA A 502 O1 161.2 90.8 101.1 REMARK 620 5 OGA A 502 O2' 85.9 165.4 92.6 76.0 REMARK 620 6 HOH A 741 O 85.0 87.3 163.5 92.8 99.3 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 TRS A 503 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: 6F4Q RELATED DB: PDB REMARK 900 RELATED ID: 6F4R RELATED DB: PDB REMARK 900 RELATED ID: 6F4S RELATED DB: PDB REMARK 900 RELATED ID: 6F4T RELATED DB: PDB DBREF 6F4P A 183 416 UNP Q8N371 KDM8_HUMAN 183 416 DBREF 6F4P B 135 150 UNP P62753 RS6_HUMAN 129 144 SEQADV 6F4P HIS A 162 UNP Q8N371 EXPRESSION TAG SEQADV 6F4P HIS A 163 UNP Q8N371 EXPRESSION TAG SEQADV 6F4P HIS A 164 UNP Q8N371 EXPRESSION TAG SEQADV 6F4P HIS A 165 UNP Q8N371 EXPRESSION TAG SEQADV 6F4P HIS A 166 UNP Q8N371 EXPRESSION TAG SEQADV 6F4P HIS A 167 UNP Q8N371 EXPRESSION TAG SEQADV 6F4P SER A 168 UNP Q8N371 EXPRESSION TAG SEQADV 6F4P SER A 169 UNP Q8N371 EXPRESSION TAG SEQADV 6F4P GLY A 170 UNP Q8N371 EXPRESSION TAG SEQADV 6F4P VAL A 171 UNP Q8N371 EXPRESSION TAG SEQADV 6F4P ASP A 172 UNP Q8N371 EXPRESSION TAG SEQADV 6F4P LEU A 173 UNP Q8N371 EXPRESSION TAG SEQADV 6F4P GLY A 174 UNP Q8N371 EXPRESSION TAG SEQADV 6F4P THR A 175 UNP Q8N371 EXPRESSION TAG SEQADV 6F4P GLU A 176 UNP Q8N371 EXPRESSION TAG SEQADV 6F4P ASN A 177 UNP Q8N371 EXPRESSION TAG SEQADV 6F4P LEU A 178 UNP Q8N371 EXPRESSION TAG SEQADV 6F4P TYR A 179 UNP Q8N371 EXPRESSION TAG SEQADV 6F4P PHE A 180 UNP Q8N371 EXPRESSION TAG SEQADV 6F4P GLN A 181 UNP Q8N371 EXPRESSION TAG SEQADV 6F4P SER A 182 UNP Q8N371 EXPRESSION TAG SEQADV 6F4P ALA A 217 UNP Q8N371 CYS 217 ENGINEERED MUTATION SEQADV 6F4P ALA A 232 UNP Q8N371 CYS 232 ENGINEERED MUTATION SEQADV 6F4P ALA A 295 UNP Q8N371 CYS 295 ENGINEERED MUTATION SEQADV 6F4P ALA A 384 UNP Q8N371 CYS 384 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 ALA 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 ALA 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 16 VAL PRO ARG ARG LEU GLY PRO LYS ARG ALA SER ARG ILE SEQRES 2 B 16 ARG LYS LEU HET MN A 501 1 HET OGA A 502 13 HET TRS A 503 20 HETNAM MN MANGANESE (II) ION HETNAM OGA N-OXALYLGLYCINE HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 3 MN MN 2+ FORMUL 4 OGA C4 H5 N O5 FORMUL 5 TRS C4 H12 N O3 1+ FORMUL 6 HOH *329(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 5 SER A 182 THR A 183 0 SHEET 2 AA1 5 LEU A 382 LEU A 386 1 O SER A 383 N SER A 182 SHEET 3 AA1 5 LYS A 336 TYR A 341 -1 N LYS A 336 O LEU A 386 SHEET 4 AA1 5 TRP A 399 ALA A 404 -1 O ARG A 403 N TYR A 337 SHEET 5 AA1 5 ILE A 317 HIS A 321 -1 N HIS A 321 O HIS A 400 SHEET 1 AA2 9 ARG A 186 HIS A 188 0 SHEET 2 AA2 9 VAL A 206 LYS A 209 1 O LYS A 209 N LEU A 187 SHEET 3 AA2 9 ILE A 391 ILE A 394 -1 O PHE A 393 N VAL A 206 SHEET 4 AA2 9 GLN A 326 MET A 333 -1 N LEU A 329 O LEU A 392 SHEET 5 AA2 9 SER A 408 TRP A 415 -1 O VAL A 411 N VAL A 330 SHEET 6 AA2 9 THR A 306 GLY A 312 -1 N GLY A 312 O SER A 408 SHEET 7 AA2 9 GLY A 271 HIS A 276 -1 N HIS A 276 O ALA A 309 SHEET 8 AA2 9 THR A 234 VAL A 239 -1 N GLU A 238 O TYR A 272 SHEET 9 AA2 9 SER A 249 THR A 254 -1 O SER A 249 N VAL A 239 LINK NE2 HIS A 321 MN MN A 501 1555 1555 2.23 LINK OD2 ASP A 323 MN MN A 501 1555 1555 2.12 LINK NE2 HIS A 400 MN MN A 501 1555 1555 2.29 LINK MN MN A 501 O1 OGA A 502 1555 1555 2.19 LINK MN MN A 501 O2' OGA A 502 1555 1555 2.17 LINK MN MN A 501 O HOH A 741 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 A 741 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 742 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 604 HOH A 639 HOH A 664 SITE 4 AC3 13 HOH A 677 CRYST1 49.283 64.925 78.037 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 0.020291 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015402 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012814 0.00000