HEADER OXIDOREDUCTASE 13-AUG-15 5D6W TITLE CRYSTAL STRUCTURE OF DOUBLE TUDOR DOMAIN OF HUMAN LYSINE DEMETHYLASE TITLE 2 KDM4A COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 4A; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3A, COMPND 5 JUMONJI DOMAIN-CONTAINING PROTEIN 2A; COMPND 6 EC: 1.14.11.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS DOUBLE TUDOR DOMAIN, READER DOMAIN, STRUCTURAL GENOMICS, PSI-2, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, ENZYME DISCOVERY FOR NATURAL PRODUCT KEYWDS 3 BIOSYNTHESIS, NATPRO, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR F.WANG,Z.SU,J.M.DENU,G.N.PHILLIPS JR.,ENZYME DISCOVERY FOR NATURAL AUTHOR 2 PRODUCT BIOSYNTHESIS (NATPRO) REVDAT 5 06-MAR-24 5D6W 1 REMARK REVDAT 4 25-DEC-19 5D6W 1 REMARK REVDAT 3 20-SEP-17 5D6W 1 REMARK REVDAT 2 07-DEC-16 5D6W 1 JRNL REVDAT 1 25-NOV-15 5D6W 0 JRNL AUTH Z.SU,F.WANG,J.H.LEE,K.E.STEPHENS,R.PAPAZYAN,E.VORONINA, JRNL AUTH 2 K.A.KRAUTKRAMER,A.RAMAN,J.J.THORPE,M.D.BOERSMA, JRNL AUTH 3 V.I.KUZNETSOV,M.D.MILLER,S.D.TAVERNA,G.N.PHILLIPS,J.M.DENU JRNL TITL READER DOMAIN SPECIFICITY AND LYSINE DEMETHYLASE-4 FAMILY JRNL TITL 2 FUNCTION. JRNL REF NAT COMMUN V. 7 13387 2016 JRNL REFN ESSN 2041-1723 JRNL PMID 27841353 JRNL DOI 10.1038/NCOMMS13387 REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 108213 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.660 REMARK 3 FREE R VALUE TEST SET COUNT : 3965 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 36.0900 - 6.0399 0.99 3725 125 0.1616 0.1924 REMARK 3 2 6.0399 - 4.7976 1.00 3721 144 0.1290 0.1215 REMARK 3 3 4.7976 - 4.1922 1.00 3768 144 0.1232 0.1337 REMARK 3 4 4.1922 - 3.8094 1.00 3711 136 0.1251 0.1484 REMARK 3 5 3.8094 - 3.5366 1.00 3705 138 0.1373 0.1678 REMARK 3 6 3.5366 - 3.3282 1.00 3757 146 0.1625 0.2046 REMARK 3 7 3.3282 - 3.1617 1.00 3727 144 0.1737 0.2310 REMARK 3 8 3.1617 - 3.0241 1.00 3715 136 0.1896 0.2696 REMARK 3 9 3.0241 - 2.9077 1.00 3739 144 0.1995 0.2203 REMARK 3 10 2.9077 - 2.8074 1.00 3722 146 0.1839 0.2366 REMARK 3 11 2.8074 - 2.7197 1.00 3717 148 0.1877 0.2093 REMARK 3 12 2.7197 - 2.6420 1.00 3716 146 0.1767 0.2269 REMARK 3 13 2.6420 - 2.5724 1.00 3749 142 0.1892 0.2007 REMARK 3 14 2.5724 - 2.5097 1.00 3717 136 0.1899 0.1949 REMARK 3 15 2.5097 - 2.4526 1.00 3739 129 0.1935 0.2073 REMARK 3 16 2.4526 - 2.4005 1.00 3771 148 0.2019 0.2497 REMARK 3 17 2.4005 - 2.3525 1.00 3694 146 0.1834 0.1811 REMARK 3 18 2.3525 - 2.3081 1.00 3747 144 0.1849 0.2458 REMARK 3 19 2.3081 - 2.2669 1.00 3735 146 0.1850 0.2118 REMARK 3 20 2.2669 - 2.2284 1.00 3738 142 0.2190 0.2767 REMARK 3 21 2.2284 - 2.1925 1.00 3664 142 0.2072 0.2273 REMARK 3 22 2.1925 - 2.1588 1.00 3761 134 0.2152 0.3153 REMARK 3 23 2.1588 - 2.1270 1.00 3747 147 0.2116 0.2365 REMARK 3 24 2.1270 - 2.0971 1.00 3700 151 0.2178 0.1912 REMARK 3 25 2.0971 - 2.0687 1.00 3730 134 0.2306 0.2307 REMARK 3 26 2.0687 - 2.0419 1.00 3718 148 0.2365 0.3061 REMARK 3 27 2.0419 - 2.0163 1.00 3699 144 0.2567 0.2704 REMARK 3 28 2.0163 - 1.9921 0.96 3616 135 0.2720 0.2746 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.030 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 3928 REMARK 3 ANGLE : 1.074 5349 REMARK 3 CHIRALITY : 0.051 565 REMARK 3 PLANARITY : 0.005 731 REMARK 3 DIHEDRAL : 16.728 1431 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 897 THROUGH 1011) REMARK 3 ORIGIN FOR THE GROUP (A): -42.4448 -10.4689 -54.9464 REMARK 3 T TENSOR REMARK 3 T11: 0.2798 T22: 0.3548 REMARK 3 T33: 0.2794 T12: -0.0534 REMARK 3 T13: -0.0066 T23: 0.0423 REMARK 3 L TENSOR REMARK 3 L11: 0.0363 L22: 1.7117 REMARK 3 L33: 3.0662 L12: 0.4667 REMARK 3 L13: 0.8437 L23: 2.1146 REMARK 3 S TENSOR REMARK 3 S11: 0.0070 S12: 0.0608 S13: -0.0352 REMARK 3 S21: 0.0884 S22: 0.0376 S23: -0.0740 REMARK 3 S31: 0.1677 S32: -0.1462 S33: -0.0551 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 897 THROUGH 1011) REMARK 3 ORIGIN FOR THE GROUP (A): -32.7144 21.8343 -20.0900 REMARK 3 T TENSOR REMARK 3 T11: 0.2515 T22: 0.3745 REMARK 3 T33: 0.2571 T12: -0.0261 REMARK 3 T13: 0.0134 T23: 0.0224 REMARK 3 L TENSOR REMARK 3 L11: 0.4943 L22: 1.9079 REMARK 3 L33: 2.3198 L12: 0.8544 REMARK 3 L13: 1.1367 L23: 2.0456 REMARK 3 S TENSOR REMARK 3 S11: 0.0703 S12: -0.1247 S13: 0.0167 REMARK 3 S21: -0.0069 S22: -0.1457 S23: 0.0799 REMARK 3 S31: -0.0733 S32: -0.0653 S33: 0.0899 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'C' AND RESID 897 THROUGH 1011) REMARK 3 ORIGIN FOR THE GROUP (A): -14.9833 11.3219 -27.6833 REMARK 3 T TENSOR REMARK 3 T11: 0.2634 T22: 0.2954 REMARK 3 T33: 0.3713 T12: 0.0034 REMARK 3 T13: -0.0288 T23: 0.0505 REMARK 3 L TENSOR REMARK 3 L11: 0.2690 L22: 3.5919 REMARK 3 L33: 0.5164 L12: 1.3513 REMARK 3 L13: 0.3637 L23: 1.4282 REMARK 3 S TENSOR REMARK 3 S11: 0.0712 S12: -0.0333 S13: -0.1256 REMARK 3 S21: -0.0831 S22: 0.0436 S23: -0.1281 REMARK 3 S31: 0.0131 S32: -0.0047 S33: -0.1462 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN 'D' AND RESID 897 THROUGH 1011) REMARK 3 ORIGIN FOR THE GROUP (A): -45.0010 -32.0159 -30.5086 REMARK 3 T TENSOR REMARK 3 T11: 0.3303 T22: 0.2753 REMARK 3 T33: 0.2939 T12: -0.0011 REMARK 3 T13: -0.0756 T23: 0.0178 REMARK 3 L TENSOR REMARK 3 L11: 2.3792 L22: 2.2671 REMARK 3 L33: 0.2717 L12: 2.2459 REMARK 3 L13: -1.0127 L23: -0.6898 REMARK 3 S TENSOR REMARK 3 S11: -0.1508 S12: 0.1137 S13: 0.1168 REMARK 3 S21: -0.0755 S22: 0.0636 S23: -0.0061 REMARK 3 S31: 0.0326 S32: -0.0102 S33: 0.0862 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A REMARK 3 SELECTION : CHAIN B REMARK 3 ATOM PAIRS NUMBER : 2227 REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: CHAIN A REMARK 3 SELECTION : CHAIN C REMARK 3 ATOM PAIRS NUMBER : 2227 REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 3 REMARK 3 REFERENCE SELECTION: CHAIN A REMARK 3 SELECTION : CHAIN D REMARK 3 ATOM PAIRS NUMBER : 2227 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5D6W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000211854. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 108314 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.190 REMARK 200 R MERGE (I) : 0.12700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.00600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.940 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION (30MG/ML KDM4A DTD, REMARK 280 20MM HEPES PH 7.5, 150MM NACL AND 0.5MM TCEP) MIXED IN A 1:1 REMARK 280 RATIO WITH THE WELL SOLUTION (1.0M AMMONIUM TARTRATE DIBASIC AND REMARK 280 0.1M SODIUM ACETATE TRIHYDRATE PH4.6) CRYOPROTECTED WITH REMARK 280 ADDITIONAL 20% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 95.32200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 55.03418 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 38.98533 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 95.32200 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 55.03418 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 38.98533 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 95.32200 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 55.03418 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 38.98533 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 95.32200 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 55.03418 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 38.98533 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 95.32200 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 55.03418 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 38.98533 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 95.32200 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 55.03418 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 38.98533 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 110.06836 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 77.97067 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 110.06836 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 77.97067 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 110.06836 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 77.97067 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 110.06836 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 77.97067 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 110.06836 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 77.97067 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 110.06836 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 77.97067 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 891 REMARK 465 SER A 892 REMARK 465 HIS A 893 REMARK 465 MET A 894 REMARK 465 ALA A 895 REMARK 465 LEU A 896 REMARK 465 GLY B 891 REMARK 465 SER B 892 REMARK 465 HIS B 893 REMARK 465 MET B 894 REMARK 465 ALA B 895 REMARK 465 LEU B 896 REMARK 465 GLY C 891 REMARK 465 SER C 892 REMARK 465 HIS C 893 REMARK 465 MET C 894 REMARK 465 ALA C 895 REMARK 465 LEU C 896 REMARK 465 GLY D 891 REMARK 465 SER D 892 REMARK 465 HIS D 893 REMARK 465 MET D 894 REMARK 465 ALA D 895 REMARK 465 LEU D 896 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 LYS A 976 O HOH A 1201 2.05 REMARK 500 O HOH A 1315 O HOH B 1314 2.09 REMARK 500 O HOH D 1267 O HOH D 1301 2.13 REMARK 500 O11 SRT D 1101 O HOH D 1201 2.15 REMARK 500 O HOH C 1233 O HOH C 1301 2.15 REMARK 500 O HOH B 1273 O HOH B 1295 2.16 REMARK 500 O HOH D 1254 O HOH D 1292 2.16 REMARK 500 O1 SRT B 1101 O HOH B 1201 2.17 REMARK 500 O11 SRT A 1101 O HOH A 1202 2.17 REMARK 500 NE2 GLN D 984 O HOH D 1202 2.18 REMARK 500 O HOH B 1231 O HOH B 1287 2.18 REMARK 500 O HOH C 1230 O HOH C 1296 2.19 REMARK 500 O HOH B 1244 O HOH B 1290 2.19 REMARK 500 O ASN A 931 O HOH A 1201 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 1207 O HOH D 1220 8455 2.06 REMARK 500 O HOH A 1271 O HOH B 1219 5554 2.14 REMARK 500 O HOH B 1292 O HOH D 1211 16554 2.17 REMARK 500 O HOH A 1211 O HOH B 1299 15444 2.19 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 ASN A 940 41.32 -143.19 REMARK 500 ASN B 940 41.13 -143.47 REMARK 500 ASN C 940 41.46 -143.23 REMARK 500 ASN D 940 41.06 -142.53 REMARK 500 VAL D 978 -60.66 -102.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SRT A 1101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SRT B 1101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SRT C 1101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SRT D 1101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5D6X RELATED DB: PDB REMARK 900 RELATED ID: 5D6Y RELATED DB: PDB DBREF 5D6W A 895 1011 UNP O75164 KDM4A_HUMAN 895 1011 DBREF 5D6W B 895 1011 UNP O75164 KDM4A_HUMAN 895 1011 DBREF 5D6W C 895 1011 UNP O75164 KDM4A_HUMAN 895 1011 DBREF 5D6W D 895 1011 UNP O75164 KDM4A_HUMAN 895 1011 SEQADV 5D6W GLY A 891 UNP O75164 EXPRESSION TAG SEQADV 5D6W SER A 892 UNP O75164 EXPRESSION TAG SEQADV 5D6W HIS A 893 UNP O75164 EXPRESSION TAG SEQADV 5D6W MET A 894 UNP O75164 EXPRESSION TAG SEQADV 5D6W GLY B 891 UNP O75164 EXPRESSION TAG SEQADV 5D6W SER B 892 UNP O75164 EXPRESSION TAG SEQADV 5D6W HIS B 893 UNP O75164 EXPRESSION TAG SEQADV 5D6W MET B 894 UNP O75164 EXPRESSION TAG SEQADV 5D6W GLY C 891 UNP O75164 EXPRESSION TAG SEQADV 5D6W SER C 892 UNP O75164 EXPRESSION TAG SEQADV 5D6W HIS C 893 UNP O75164 EXPRESSION TAG SEQADV 5D6W MET C 894 UNP O75164 EXPRESSION TAG SEQADV 5D6W GLY D 891 UNP O75164 EXPRESSION TAG SEQADV 5D6W SER D 892 UNP O75164 EXPRESSION TAG SEQADV 5D6W HIS D 893 UNP O75164 EXPRESSION TAG SEQADV 5D6W MET D 894 UNP O75164 EXPRESSION TAG SEQRES 1 A 121 GLY SER HIS MET ALA LEU GLN SER ILE THR ALA GLY GLN SEQRES 2 A 121 LYS VAL ILE SER LYS HIS LYS ASN GLY ARG PHE TYR GLN SEQRES 3 A 121 CYS GLU VAL VAL ARG LEU THR THR GLU THR PHE TYR GLU SEQRES 4 A 121 VAL ASN PHE ASP ASP GLY SER PHE SER ASP ASN LEU TYR SEQRES 5 A 121 PRO GLU ASP ILE VAL SER GLN ASP CYS LEU GLN PHE GLY SEQRES 6 A 121 PRO PRO ALA GLU GLY GLU VAL VAL GLN VAL ARG TRP THR SEQRES 7 A 121 ASP GLY GLN VAL TYR GLY ALA LYS PHE VAL ALA SER HIS SEQRES 8 A 121 PRO ILE GLN MET TYR GLN VAL GLU PHE GLU ASP GLY SER SEQRES 9 A 121 GLN LEU VAL VAL LYS ARG ASP ASP VAL TYR THR LEU ASP SEQRES 10 A 121 GLU GLU LEU PRO SEQRES 1 B 121 GLY SER HIS MET ALA LEU GLN SER ILE THR ALA GLY GLN SEQRES 2 B 121 LYS VAL ILE SER LYS HIS LYS ASN GLY ARG PHE TYR GLN SEQRES 3 B 121 CYS GLU VAL VAL ARG LEU THR THR GLU THR PHE TYR GLU SEQRES 4 B 121 VAL ASN PHE ASP ASP GLY SER PHE SER ASP ASN LEU TYR SEQRES 5 B 121 PRO GLU ASP ILE VAL SER GLN ASP CYS LEU GLN PHE GLY SEQRES 6 B 121 PRO PRO ALA GLU GLY GLU VAL VAL GLN VAL ARG TRP THR SEQRES 7 B 121 ASP GLY GLN VAL TYR GLY ALA LYS PHE VAL ALA SER HIS SEQRES 8 B 121 PRO ILE GLN MET TYR GLN VAL GLU PHE GLU ASP GLY SER SEQRES 9 B 121 GLN LEU VAL VAL LYS ARG ASP ASP VAL TYR THR LEU ASP SEQRES 10 B 121 GLU GLU LEU PRO SEQRES 1 C 121 GLY SER HIS MET ALA LEU GLN SER ILE THR ALA GLY GLN SEQRES 2 C 121 LYS VAL ILE SER LYS HIS LYS ASN GLY ARG PHE TYR GLN SEQRES 3 C 121 CYS GLU VAL VAL ARG LEU THR THR GLU THR PHE TYR GLU SEQRES 4 C 121 VAL ASN PHE ASP ASP GLY SER PHE SER ASP ASN LEU TYR SEQRES 5 C 121 PRO GLU ASP ILE VAL SER GLN ASP CYS LEU GLN PHE GLY SEQRES 6 C 121 PRO PRO ALA GLU GLY GLU VAL VAL GLN VAL ARG TRP THR SEQRES 7 C 121 ASP GLY GLN VAL TYR GLY ALA LYS PHE VAL ALA SER HIS SEQRES 8 C 121 PRO ILE GLN MET TYR GLN VAL GLU PHE GLU ASP GLY SER SEQRES 9 C 121 GLN LEU VAL VAL LYS ARG ASP ASP VAL TYR THR LEU ASP SEQRES 10 C 121 GLU GLU LEU PRO SEQRES 1 D 121 GLY SER HIS MET ALA LEU GLN SER ILE THR ALA GLY GLN SEQRES 2 D 121 LYS VAL ILE SER LYS HIS LYS ASN GLY ARG PHE TYR GLN SEQRES 3 D 121 CYS GLU VAL VAL ARG LEU THR THR GLU THR PHE TYR GLU SEQRES 4 D 121 VAL ASN PHE ASP ASP GLY SER PHE SER ASP ASN LEU TYR SEQRES 5 D 121 PRO GLU ASP ILE VAL SER GLN ASP CYS LEU GLN PHE GLY SEQRES 6 D 121 PRO PRO ALA GLU GLY GLU VAL VAL GLN VAL ARG TRP THR SEQRES 7 D 121 ASP GLY GLN VAL TYR GLY ALA LYS PHE VAL ALA SER HIS SEQRES 8 D 121 PRO ILE GLN MET TYR GLN VAL GLU PHE GLU ASP GLY SER SEQRES 9 D 121 GLN LEU VAL VAL LYS ARG ASP ASP VAL TYR THR LEU ASP SEQRES 10 D 121 GLU GLU LEU PRO HET SRT A1101 10 HET SRT B1101 10 HET SRT C1101 10 HET SRT D1101 10 HETNAM SRT S,R MESO-TARTARIC ACID FORMUL 5 SRT 4(C4 H6 O6) FORMUL 9 HOH *515(H2 O) HELIX 1 AA1 TYR A 942 ILE A 946 5 5 HELIX 2 AA2 ASP A 950 GLY A 955 1 6 HELIX 3 AA3 LYS A 999 VAL A 1003 5 5 HELIX 4 AA4 TYR B 942 ILE B 946 5 5 HELIX 5 AA5 ASP B 950 GLY B 955 1 6 HELIX 6 AA6 LYS B 999 VAL B 1003 5 5 HELIX 7 AA7 TYR C 942 ILE C 946 5 5 HELIX 8 AA8 ASP C 950 GLY C 955 1 6 HELIX 9 AA9 LYS C 999 VAL C 1003 5 5 HELIX 10 AB1 TYR D 942 ILE D 946 5 5 HELIX 11 AB2 ASP D 950 GLY D 955 1 6 HELIX 12 AB3 LYS D 999 VAL D 1003 5 5 SHEET 1 AA1 4 LYS A 904 LYS A 908 0 SHEET 2 AA1 4 PHE A 914 PHE A 932 -1 O CYS A 917 N VAL A 905 SHEET 3 AA1 4 VAL A 972 PHE A 990 -1 O ALA A 979 N GLU A 929 SHEET 4 AA1 4 VAL A 962 ARG A 966 -1 N VAL A 963 O ALA A 975 SHEET 1 AA2 4 PHE A 937 LEU A 941 0 SHEET 2 AA2 4 PHE A 914 PHE A 932 -1 N TYR A 928 O LEU A 941 SHEET 3 AA2 4 VAL A 972 PHE A 990 -1 O ALA A 979 N GLU A 929 SHEET 4 AA2 4 GLN A 995 VAL A 998 -1 O VAL A 998 N TYR A 986 SHEET 1 AA3 4 LYS B 904 LYS B 908 0 SHEET 2 AA3 4 PHE B 914 PHE B 932 -1 O CYS B 917 N VAL B 905 SHEET 3 AA3 4 VAL B 972 PHE B 990 -1 O VAL B 978 N GLU B 929 SHEET 4 AA3 4 VAL B 962 ARG B 966 -1 N VAL B 965 O TYR B 973 SHEET 1 AA4 4 PHE B 937 LEU B 941 0 SHEET 2 AA4 4 PHE B 914 PHE B 932 -1 N TYR B 928 O LEU B 941 SHEET 3 AA4 4 VAL B 972 PHE B 990 -1 O VAL B 978 N GLU B 929 SHEET 4 AA4 4 GLN B 995 VAL B 998 -1 O LEU B 996 N VAL B 988 SHEET 1 AA5 4 LYS C 904 LYS C 908 0 SHEET 2 AA5 4 PHE C 914 PHE C 932 -1 O CYS C 917 N VAL C 905 SHEET 3 AA5 4 VAL C 972 PHE C 990 -1 O ALA C 979 N GLU C 929 SHEET 4 AA5 4 VAL C 962 ARG C 966 -1 N VAL C 965 O TYR C 973 SHEET 1 AA6 4 PHE C 937 LEU C 941 0 SHEET 2 AA6 4 PHE C 914 PHE C 932 -1 N TYR C 928 O LEU C 941 SHEET 3 AA6 4 VAL C 972 PHE C 990 -1 O ALA C 979 N GLU C 929 SHEET 4 AA6 4 GLN C 995 VAL C 998 -1 O VAL C 998 N TYR C 986 SHEET 1 AA7 4 LYS D 904 LYS D 908 0 SHEET 2 AA7 4 PHE D 914 PHE D 932 -1 O CYS D 917 N VAL D 905 SHEET 3 AA7 4 VAL D 972 PHE D 990 -1 O ALA D 979 N GLU D 929 SHEET 4 AA7 4 VAL D 962 ARG D 966 -1 N VAL D 963 O ALA D 975 SHEET 1 AA8 4 PHE D 937 LEU D 941 0 SHEET 2 AA8 4 PHE D 914 PHE D 932 -1 N TYR D 928 O LEU D 941 SHEET 3 AA8 4 VAL D 972 PHE D 990 -1 O ALA D 979 N GLU D 929 SHEET 4 AA8 4 GLN D 995 VAL D 998 -1 O LEU D 996 N VAL D 988 SITE 1 AC1 7 LYS A 910 GLY A 993 SER A 994 GLN A 995 SITE 2 AC1 7 HOH A1202 HOH A1241 HOH A1246 SITE 1 AC2 7 LYS B 910 GLY B 993 SER B 994 GLN B 995 SITE 2 AC2 7 HOH B1201 HOH B1226 HOH B1267 SITE 1 AC3 7 LYS C 910 ASP C 992 GLY C 993 SER C 994 SITE 2 AC3 7 GLN C 995 HOH C1210 HOH C1239 SITE 1 AC4 7 LYS D 910 GLY D 993 SER D 994 GLN D 995 SITE 2 AC4 7 HOH D1201 HOH D1223 HOH D1265 CRYST1 190.644 190.644 116.956 90.00 90.00 120.00 H 3 2 72 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 0.005245 0.003028 0.000000 0.00000 SCALE2 0.000000 0.006057 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008550 0.00000