HEADER OXIDOREDUCTASE 29-NOV-17 6F4M TITLE HUMAN JMJD5 IN ITS APO FORM. 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 OTHER_DETAILS: CATALYTIC DOMAIN (RESIDUES 183-416) 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 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 6F4M 1 REMARK REVDAT 1 04-APR-18 6F4M 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. 1.71 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 25366 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 1246 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 48.2328 - 3.5471 1.00 2855 159 0.1541 0.1575 REMARK 3 2 3.5471 - 2.8155 1.00 2733 146 0.1586 0.1852 REMARK 3 3 2.8155 - 2.4596 1.00 2731 103 0.1694 0.1905 REMARK 3 4 2.4596 - 2.2348 1.00 2694 143 0.1659 0.1885 REMARK 3 5 2.2348 - 2.0746 1.00 2681 142 0.1664 0.1963 REMARK 3 6 2.0746 - 1.9523 1.00 2656 152 0.1724 0.1982 REMARK 3 7 1.9523 - 1.8545 1.00 2637 156 0.2139 0.2440 REMARK 3 8 1.8545 - 1.7738 1.00 2657 138 0.2464 0.2755 REMARK 3 9 1.7738 - 1.7055 0.93 2476 107 0.2967 0.3679 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 56.90 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.460 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.08000 REMARK 3 B22 (A**2) : -0.53000 REMARK 3 B33 (A**2) : 0.61000 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 : 0.005 2043 REMARK 3 ANGLE : 0.764 2802 REMARK 3 CHIRALITY : 0.053 294 REMARK 3 PLANARITY : 0.005 370 REMARK 3 DIHEDRAL : 16.671 1211 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): -25.4813 6.5216 -15.0789 REMARK 3 T TENSOR REMARK 3 T11: 0.1767 T22: 0.2719 REMARK 3 T33: 0.2439 T12: -0.0614 REMARK 3 T13: 0.0157 T23: 0.0183 REMARK 3 L TENSOR REMARK 3 L11: 1.6067 L22: 1.5158 REMARK 3 L33: 1.2918 L12: 0.1062 REMARK 3 L13: 0.1287 L23: 1.0386 REMARK 3 S TENSOR REMARK 3 S11: 0.0016 S12: 0.1113 S13: -0.1530 REMARK 3 S21: 0.0518 S22: 0.1081 S23: 0.3281 REMARK 3 S31: 0.4903 S32: -0.6188 S33: 0.0148 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 212:230) REMARK 3 ORIGIN FOR THE GROUP (A): -10.4597 17.4790 -33.0097 REMARK 3 T TENSOR REMARK 3 T11: 0.2498 T22: 0.2008 REMARK 3 T33: 0.1884 T12: -0.0256 REMARK 3 T13: -0.0062 T23: -0.0016 REMARK 3 L TENSOR REMARK 3 L11: 0.6661 L22: 0.4309 REMARK 3 L33: 0.5585 L12: 0.0776 REMARK 3 L13: 0.4989 L23: -0.4449 REMARK 3 S TENSOR REMARK 3 S11: -0.0454 S12: -0.0939 S13: 0.0169 REMARK 3 S21: -0.2449 S22: 0.0775 S23: 0.0037 REMARK 3 S31: 0.1584 S32: -0.0754 S33: 0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 231:254) REMARK 3 ORIGIN FOR THE GROUP (A): 4.2010 24.3980 -16.2739 REMARK 3 T TENSOR REMARK 3 T11: 0.2268 T22: 0.2359 REMARK 3 T33: 0.2198 T12: -0.0306 REMARK 3 T13: -0.0451 T23: -0.0088 REMARK 3 L TENSOR REMARK 3 L11: 1.7349 L22: 2.1365 REMARK 3 L33: 1.0806 L12: 0.6203 REMARK 3 L13: -0.9475 L23: 0.7328 REMARK 3 S TENSOR REMARK 3 S11: 0.1001 S12: -0.3804 S13: -0.0743 REMARK 3 S21: 0.4740 S22: 0.0115 S23: -0.0558 REMARK 3 S31: -0.0772 S32: 0.0951 S33: 0.0001 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 255:277) REMARK 3 ORIGIN FOR THE GROUP (A): 4.2330 21.6692 -22.1603 REMARK 3 T TENSOR REMARK 3 T11: 0.1835 T22: 0.2635 REMARK 3 T33: 0.2369 T12: -0.0139 REMARK 3 T13: -0.0218 T23: -0.0038 REMARK 3 L TENSOR REMARK 3 L11: 1.5049 L22: 2.1814 REMARK 3 L33: 1.6476 L12: 1.2808 REMARK 3 L13: 0.5854 L23: -0.7889 REMARK 3 S TENSOR REMARK 3 S11: 0.0318 S12: -0.6273 S13: 0.2663 REMARK 3 S21: 0.3948 S22: -0.0950 S23: -0.3257 REMARK 3 S31: -0.0819 S32: 0.2638 S33: 0.0037 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 278:305) REMARK 3 ORIGIN FOR THE GROUP (A): -18.6384 24.0581 -23.1061 REMARK 3 T TENSOR REMARK 3 T11: 0.2807 T22: 0.2515 REMARK 3 T33: 0.3254 T12: 0.0082 REMARK 3 T13: 0.0449 T23: -0.0251 REMARK 3 L TENSOR REMARK 3 L11: 1.1768 L22: 0.7087 REMARK 3 L33: 1.2489 L12: 0.3004 REMARK 3 L13: 0.6043 L23: -0.5322 REMARK 3 S TENSOR REMARK 3 S11: 0.1966 S12: -0.0103 S13: 0.7118 REMARK 3 S21: 0.3359 S22: 0.0187 S23: 0.2228 REMARK 3 S31: -0.5712 S32: -0.3217 S33: 0.0036 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 306:312) REMARK 3 ORIGIN FOR THE GROUP (A): -9.4228 21.0854 -20.7106 REMARK 3 T TENSOR REMARK 3 T11: 0.2618 T22: 0.1834 REMARK 3 T33: 0.3258 T12: 0.0191 REMARK 3 T13: 0.0694 T23: -0.0298 REMARK 3 L TENSOR REMARK 3 L11: 1.8258 L22: 0.2131 REMARK 3 L33: 0.9224 L12: -0.7489 REMARK 3 L13: -1.2699 L23: 0.4278 REMARK 3 S TENSOR REMARK 3 S11: -0.3315 S12: -0.3137 S13: 0.0857 REMARK 3 S21: 0.6538 S22: 0.2424 S23: -0.0341 REMARK 3 S31: -0.0400 S32: 0.3103 S33: -0.0034 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 313:325) REMARK 3 ORIGIN FOR THE GROUP (A): -6.3657 14.7654 -11.0434 REMARK 3 T TENSOR REMARK 3 T11: 0.2002 T22: 0.2303 REMARK 3 T33: 0.2029 T12: -0.0188 REMARK 3 T13: 0.0077 T23: -0.0102 REMARK 3 L TENSOR REMARK 3 L11: 0.4582 L22: 0.1271 REMARK 3 L33: 0.8187 L12: 0.0395 REMARK 3 L13: 0.5423 L23: -0.1246 REMARK 3 S TENSOR REMARK 3 S11: 0.0646 S12: -0.0737 S13: 0.1539 REMARK 3 S21: 0.1417 S22: -0.1830 S23: -0.1698 REMARK 3 S31: -0.2156 S32: 0.0570 S33: -0.0001 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 326:341) REMARK 3 ORIGIN FOR THE GROUP (A): -11.1768 9.8522 -16.4075 REMARK 3 T TENSOR REMARK 3 T11: 0.1743 T22: 0.1423 REMARK 3 T33: 0.1513 T12: -0.0172 REMARK 3 T13: -0.0019 T23: 0.0184 REMARK 3 L TENSOR REMARK 3 L11: 1.1282 L22: 0.4906 REMARK 3 L33: 0.2143 L12: 0.2347 REMARK 3 L13: 0.1303 L23: -0.2376 REMARK 3 S TENSOR REMARK 3 S11: 0.0406 S12: 0.0410 S13: -0.0348 REMARK 3 S21: 0.0073 S22: -0.1013 S23: -0.0286 REMARK 3 S31: 0.0922 S32: -0.0288 S33: 0.0000 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN A AND RESID 342:365) REMARK 3 ORIGIN FOR THE GROUP (A): -6.3868 13.8911 0.0367 REMARK 3 T TENSOR REMARK 3 T11: 0.3241 T22: 0.2140 REMARK 3 T33: 0.1756 T12: -0.0178 REMARK 3 T13: -0.0184 T23: -0.0435 REMARK 3 L TENSOR REMARK 3 L11: 1.5371 L22: 1.1075 REMARK 3 L33: 2.1030 L12: -0.7166 REMARK 3 L13: 1.0360 L23: 0.2704 REMARK 3 S TENSOR REMARK 3 S11: -0.0147 S12: -0.3164 S13: 0.0349 REMARK 3 S21: 0.0339 S22: -0.0077 S23: -0.3155 REMARK 3 S31: -0.4009 S32: 0.0294 S33: -0.0000 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN A AND RESID 366:381) REMARK 3 ORIGIN FOR THE GROUP (A): -2.2850 2.9660 0.9438 REMARK 3 T TENSOR REMARK 3 T11: 0.2659 T22: 0.2283 REMARK 3 T33: 0.2618 T12: -0.0452 REMARK 3 T13: -0.0661 T23: 0.0674 REMARK 3 L TENSOR REMARK 3 L11: 0.9084 L22: 1.3046 REMARK 3 L33: 0.7098 L12: -0.9078 REMARK 3 L13: 0.2362 L23: 0.4040 REMARK 3 S TENSOR REMARK 3 S11: 0.2682 S12: -0.1961 S13: -0.4370 REMARK 3 S21: 0.0997 S22: -0.0313 S23: -0.2547 REMARK 3 S31: 0.2543 S32: -0.0447 S33: 0.0004 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN A AND RESID 382:399) REMARK 3 ORIGIN FOR THE GROUP (A): -15.0095 8.9942 -13.2691 REMARK 3 T TENSOR REMARK 3 T11: 0.1564 T22: 0.1603 REMARK 3 T33: 0.1564 T12: -0.0234 REMARK 3 T13: 0.0076 T23: -0.0108 REMARK 3 L TENSOR REMARK 3 L11: 1.2489 L22: 0.9361 REMARK 3 L33: 0.9475 L12: -0.7270 REMARK 3 L13: 0.9384 L23: -0.9763 REMARK 3 S TENSOR REMARK 3 S11: -0.0870 S12: -0.0739 S13: 0.0514 REMARK 3 S21: -0.0165 S22: -0.0079 S23: 0.0214 REMARK 3 S31: 0.1180 S32: -0.1562 S33: -0.0000 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: (CHAIN A AND RESID 400:416) REMARK 3 ORIGIN FOR THE GROUP (A): -9.7575 14.3601 -17.9809 REMARK 3 T TENSOR REMARK 3 T11: 0.1881 T22: 0.1395 REMARK 3 T33: 0.1749 T12: -0.0088 REMARK 3 T13: 0.0135 T23: -0.0018 REMARK 3 L TENSOR REMARK 3 L11: 0.6488 L22: 0.5155 REMARK 3 L33: 1.2664 L12: 0.4737 REMARK 3 L13: -0.0215 L23: -0.6379 REMARK 3 S TENSOR REMARK 3 S11: 0.0521 S12: -0.0274 S13: 0.1789 REMARK 3 S21: 0.0510 S22: -0.1052 S23: -0.1318 REMARK 3 S31: -0.1683 S32: -0.0009 S33: -0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT TARGET: ML AND BULK SOLVENT REMARK 3 MODELLING METHOD USED: FLAT MODEL REMARK 4 REMARK 4 6F4M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1200007736. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAY-16 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 : 25416 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 48.210 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 13.00 REMARK 200 R MERGE FOR SHELL (I) : 1.60000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 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: 4GJZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 6.5, 22.5 % 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 24.51650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.03800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.21900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.03800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.51650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.21900 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 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 ASP A 299 CG OD1 OD2 REMARK 470 GLU A 301 CG CD OE1 OE2 REMARK 470 GLU A 302 CG CD OE1 OE2 REMARK 470 GLU A 303 CG CD OE1 OE2 REMARK 470 HIS A 355 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 371 CD OE1 OE2 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 61.17 37.62 REMARK 500 PHE A 199 -51.46 -130.85 REMARK 500 ILE A 263 -52.87 -120.06 REMARK 500 GLN A 275 -7.68 69.03 REMARK 500 GLN A 275 -9.64 70.06 REMARK 500 GLN A 277 65.32 -114.42 REMARK 500 GLU A 302 -124.88 61.73 REMARK 500 LYS A 397 -0.94 71.99 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 707 DISTANCE = 6.38 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES 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 REMARK 900 RELATED ID: 6F4T RELATED DB: PDB DBREF 6F4M A 182 416 UNP Q8N371 KDM8_HUMAN 182 416 SEQADV 6F4M SER A 182 UNP Q8N371 LYS 182 EXPRESSION TAG SEQADV 6F4M ALA A 217 UNP Q8N371 CYS 217 ENGINEERED MUTATION SEQADV 6F4M ALA A 232 UNP Q8N371 CYS 232 ENGINEERED MUTATION SEQADV 6F4M ALA A 295 UNP Q8N371 CYS 295 ENGINEERED MUTATION SEQADV 6F4M ALA A 384 UNP Q8N371 CYS 384 ENGINEERED MUTATION SEQRES 1 A 235 SER THR VAL PRO ARG LEU HIS ARG PRO SER LEU GLN HIS SEQRES 2 A 235 PHE ARG GLU GLN PHE LEU VAL PRO GLY ARG PRO VAL ILE SEQRES 3 A 235 LEU LYS GLY VAL ALA ASP HIS TRP PRO ALA MET GLN LYS SEQRES 4 A 235 TRP SER LEU GLU TYR ILE GLN GLU ILE ALA GLY ALA ARG SEQRES 5 A 235 THR VAL PRO VAL GLU VAL GLY SER ARG TYR THR ASP GLU SEQRES 6 A 235 GLU TRP SER GLN THR LEU MET THR VAL ASN GLU PHE ILE SEQRES 7 A 235 SER LYS TYR ILE VAL ASN GLU PRO ARG ASP VAL GLY TYR SEQRES 8 A 235 LEU ALA GLN HIS GLN LEU PHE ASP GLN ILE PRO GLU LEU SEQRES 9 A 235 LYS GLN ASP ILE SER ILE PRO ASP TYR ALA SER LEU GLY SEQRES 10 A 235 ASP GLY GLU GLU GLU GLU ILE THR ILE ASN ALA TRP PHE SEQRES 11 A 235 GLY PRO GLN GLY THR ILE SER PRO LEU HIS GLN ASP PRO SEQRES 12 A 235 GLN GLN ASN PHE LEU VAL GLN VAL MET GLY ARG LYS TYR SEQRES 13 A 235 ILE ARG LEU TYR SER PRO GLN GLU SER GLY ALA LEU TYR SEQRES 14 A 235 PRO HIS ASP THR HIS LEU LEU HIS ASN THR SER GLN VAL SEQRES 15 A 235 ASP VAL GLU ASN PRO ASP LEU GLU LYS PHE PRO LYS PHE SEQRES 16 A 235 ALA LYS ALA PRO PHE LEU SER ALA ILE LEU SER PRO GLY SEQRES 17 A 235 GLU ILE LEU PHE ILE PRO VAL LYS TYR TRP HIS TYR VAL SEQRES 18 A 235 ARG ALA LEU ASP LEU SER PHE SER VAL SER PHE TRP TRP SEQRES 19 A 235 SER FORMUL 2 HOH *207(H2 O) HELIX 1 AA1 SER A 191 PHE A 199 1 9 HELIX 2 AA2 TRP A 215 TRP A 221 1 7 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 PRO A 283 ILE A 289 5 7 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 LEU A 349 5 8 HELIX 10 AB1 PHE A 373 ALA A 379 5 7 SHEET 1 AA1 6 ARG A 186 HIS A 188 0 SHEET 2 AA1 6 VAL A 206 LYS A 209 1 O LYS A 209 N LEU A 187 SHEET 3 AA1 6 ILE A 391 ILE A 394 -1 O PHE A 393 N VAL A 206 SHEET 4 AA1 6 GLN A 326 MET A 333 -1 N LEU A 329 O LEU A 392 SHEET 5 AA1 6 SER A 408 TRP A 415 -1 O VAL A 411 N VAL A 330 SHEET 6 AA1 6 THR A 306 GLY A 312 -1 N TRP A 310 O SER A 410 SHEET 1 AA2 3 TRP A 248 THR A 254 0 SHEET 2 AA2 3 THR A 234 GLY A 240 -1 N VAL A 235 O MET A 253 SHEET 3 AA2 3 VAL A 270 LEU A 273 -1 O VAL A 270 N GLY A 240 SHEET 1 AA3 4 ILE A 317 GLN A 322 0 SHEET 2 AA3 4 TRP A 399 ALA A 404 -1 O VAL A 402 N SER A 318 SHEET 3 AA3 4 LYS A 336 TYR A 341 -1 N TYR A 341 O TRP A 399 SHEET 4 AA3 4 LEU A 382 LEU A 386 -1 O LEU A 382 N LEU A 340 SHEET 1 AA4 2 PRO A 351 HIS A 352 0 SHEET 2 AA4 2 THR A 360 SER A 361 -1 O THR A 360 N HIS A 352 CRYST1 49.033 66.438 70.076 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 0.020394 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015052 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014270 0.00000