HEADER OXIDOREDUCTASE/DNA 26-AUG-15 5DEU TITLE CRYSTAL STRUCTURE OF TET2-5HMC COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYLCYTOSINE DIOXYGENASE TET2, CHIMERIC CONSTRUCT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1129-1480, 1844-1935; COMPND 5 EC: 1.14.11.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*AP*CP*CP*AP*CP*(5HC)P*GP*GP*TP*GP*GP*T)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(P*CP*CP*AP*CP*(5HC)P*GP*GP*TP*GP*GP*T)-3'); COMPND 13 CHAIN: C; COMPND 14 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: TET2, KIAA1546, NBLA00191; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 32630; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630; SOURCE 16 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 32630 KEYWDS 5-METHYLCYTOSINE DIOXYGENASE, TET2, 5HMC, PROTEIN-DNA COMPLEX, KEYWDS 2 OXIDOREDUCTASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.HU,J.CHENG,Q.RAO,Z.LI,J.LI,Y.XU REVDAT 3 27-SEP-23 5DEU 1 JRNL REMARK REVDAT 2 18-NOV-15 5DEU 1 JRNL REVDAT 1 04-NOV-15 5DEU 0 JRNL AUTH L.HU,J.LU,J.CHENG,Q.RAO,Z.LI,H.HOU,Z.LOU,L.ZHANG,W.LI, JRNL AUTH 2 W.GONG,M.LIU,C.SUN,X.YIN,J.LI,X.TAN,P.WANG,Y.WANG,D.FANG, JRNL AUTH 3 Q.CUI,P.YANG,C.HE,H.JIANG,C.LUO,Y.XU JRNL TITL STRUCTURAL INSIGHT INTO SUBSTRATE PREFERENCE FOR JRNL TITL 2 TET-MEDIATED OXIDATION. JRNL REF NATURE V. 527 118 2015 JRNL REFN ESSN 1476-4687 JRNL PMID 26524525 JRNL DOI 10.1038/NATURE15713 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 50686 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.940 REMARK 3 FREE R VALUE TEST SET COUNT : 1995 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 42.2741 - 4.3394 0.95 3585 149 0.1653 0.1741 REMARK 3 2 4.3394 - 3.4448 0.99 3576 149 0.1474 0.1676 REMARK 3 3 3.4448 - 3.0095 1.00 3567 146 0.1738 0.2321 REMARK 3 4 3.0095 - 2.7344 1.00 3570 144 0.1918 0.2436 REMARK 3 5 2.7344 - 2.5384 1.00 3553 148 0.1965 0.2450 REMARK 3 6 2.5384 - 2.3888 1.00 3518 144 0.1908 0.2605 REMARK 3 7 2.3888 - 2.2692 1.00 3523 145 0.1834 0.2329 REMARK 3 8 2.2692 - 2.1704 1.00 3514 141 0.1847 0.2233 REMARK 3 9 2.1704 - 2.0868 1.00 3514 143 0.1821 0.2353 REMARK 3 10 2.0868 - 2.0148 1.00 3508 143 0.1916 0.2222 REMARK 3 11 2.0148 - 1.9518 1.00 3538 146 0.2078 0.2618 REMARK 3 12 1.9518 - 1.8960 0.98 3431 146 0.2177 0.2569 REMARK 3 13 1.8960 - 1.8461 0.94 3256 118 0.2459 0.2961 REMARK 3 14 1.8461 - 1.8011 0.87 3038 133 0.2763 0.2942 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.950 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.98 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 : 0.006 3873 REMARK 3 ANGLE : 1.150 5320 REMARK 3 CHIRALITY : 0.072 575 REMARK 3 PLANARITY : 0.004 612 REMARK 3 DIHEDRAL : 18.947 1504 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1132 THROUGH 1168 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.5199 14.8399 -50.0884 REMARK 3 T TENSOR REMARK 3 T11: 0.5153 T22: 0.2916 REMARK 3 T33: 0.3170 T12: -0.0370 REMARK 3 T13: -0.1138 T23: 0.0524 REMARK 3 L TENSOR REMARK 3 L11: 3.0861 L22: 4.6116 REMARK 3 L33: 3.6586 L12: 0.9006 REMARK 3 L13: -1.2436 L23: 0.2850 REMARK 3 S TENSOR REMARK 3 S11: 0.1004 S12: 0.2887 S13: 0.6260 REMARK 3 S21: -0.2838 S22: -0.0826 S23: 0.1858 REMARK 3 S31: -0.8958 S32: -0.1626 S33: -0.0052 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1169 THROUGH 1237 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.7686 1.5511 -49.6589 REMARK 3 T TENSOR REMARK 3 T11: 0.2707 T22: 0.2124 REMARK 3 T33: 0.2399 T12: 0.0230 REMARK 3 T13: -0.1006 T23: -0.0296 REMARK 3 L TENSOR REMARK 3 L11: 2.8048 L22: 2.1748 REMARK 3 L33: 2.4158 L12: 0.3386 REMARK 3 L13: 0.3405 L23: -0.1652 REMARK 3 S TENSOR REMARK 3 S11: 0.0037 S12: 0.2366 S13: 0.0110 REMARK 3 S21: -0.2882 S22: -0.0507 S23: 0.0728 REMARK 3 S31: -0.2289 S32: 0.0980 S33: 0.0445 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1238 THROUGH 1282 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.7400 -9.4191 -26.8105 REMARK 3 T TENSOR REMARK 3 T11: 0.2667 T22: 0.2478 REMARK 3 T33: 0.3832 T12: -0.0447 REMARK 3 T13: -0.0681 T23: 0.0301 REMARK 3 L TENSOR REMARK 3 L11: 2.4571 L22: 3.0080 REMARK 3 L33: 4.0494 L12: 0.2391 REMARK 3 L13: -0.8917 L23: 0.3451 REMARK 3 S TENSOR REMARK 3 S11: -0.0758 S12: -0.2931 S13: -0.2508 REMARK 3 S21: 0.4200 S22: 0.0321 S23: 0.4158 REMARK 3 S31: 0.1756 S32: -0.3478 S33: 0.0654 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1283 THROUGH 1385 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.4308 3.4451 -24.0232 REMARK 3 T TENSOR REMARK 3 T11: 0.3306 T22: 0.2428 REMARK 3 T33: 0.3295 T12: -0.0376 REMARK 3 T13: -0.1727 T23: 0.0338 REMARK 3 L TENSOR REMARK 3 L11: 1.9928 L22: 2.2184 REMARK 3 L33: 2.6666 L12: -0.3501 REMARK 3 L13: 0.4564 L23: 0.0380 REMARK 3 S TENSOR REMARK 3 S11: -0.0990 S12: -0.2713 S13: -0.0757 REMARK 3 S21: 0.4049 S22: 0.0244 S23: -0.2441 REMARK 3 S31: -0.3210 S32: 0.1963 S33: 0.0355 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1386 THROUGH 1423 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.1264 -5.7309 -40.4048 REMARK 3 T TENSOR REMARK 3 T11: 0.2118 T22: 0.1937 REMARK 3 T33: 0.3546 T12: 0.0093 REMARK 3 T13: -0.0974 T23: -0.0070 REMARK 3 L TENSOR REMARK 3 L11: 2.4863 L22: 1.1368 REMARK 3 L33: 3.2107 L12: -1.0947 REMARK 3 L13: 0.7659 L23: -1.5629 REMARK 3 S TENSOR REMARK 3 S11: 0.0467 S12: 0.0941 S13: -0.2598 REMARK 3 S21: -0.2689 S22: -0.0502 S23: 0.0860 REMARK 3 S31: 0.0797 S32: 0.0800 S33: 0.0069 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1424 THROUGH 1861 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.1796 -5.8466 -48.4610 REMARK 3 T TENSOR REMARK 3 T11: 0.3321 T22: 0.3037 REMARK 3 T33: 0.4663 T12: 0.0110 REMARK 3 T13: -0.1718 T23: -0.0697 REMARK 3 L TENSOR REMARK 3 L11: 4.8378 L22: 1.6325 REMARK 3 L33: 5.1712 L12: 0.0819 REMARK 3 L13: -3.1970 L23: -0.4657 REMARK 3 S TENSOR REMARK 3 S11: -0.3197 S12: 0.2545 S13: -0.3507 REMARK 3 S21: -0.2124 S22: 0.0513 S23: 0.4617 REMARK 3 S31: 0.3215 S32: -0.5501 S33: 0.2575 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1862 THROUGH 1921 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.3714 1.9453 -29.6610 REMARK 3 T TENSOR REMARK 3 T11: 0.2247 T22: 0.1949 REMARK 3 T33: 0.3267 T12: -0.0028 REMARK 3 T13: -0.1047 T23: 0.0183 REMARK 3 L TENSOR REMARK 3 L11: 1.4904 L22: 1.6496 REMARK 3 L33: 2.7976 L12: -0.2397 REMARK 3 L13: 0.7463 L23: -0.1597 REMARK 3 S TENSOR REMARK 3 S11: -0.0677 S12: -0.1878 S13: -0.0056 REMARK 3 S21: 0.1380 S22: -0.0293 S23: 0.0114 REMARK 3 S31: -0.3783 S32: -0.0449 S33: 0.1138 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.1735 8.9239 -15.5698 REMARK 3 T TENSOR REMARK 3 T11: 0.5393 T22: 0.2932 REMARK 3 T33: 0.3908 T12: -0.0375 REMARK 3 T13: -0.1141 T23: 0.0214 REMARK 3 L TENSOR REMARK 3 L11: 6.2875 L22: 4.1390 REMARK 3 L33: 0.3686 L12: -0.9077 REMARK 3 L13: -1.5707 L23: 0.6090 REMARK 3 S TENSOR REMARK 3 S11: 0.2189 S12: -0.3422 S13: -0.1021 REMARK 3 S21: 0.3839 S22: -0.3418 S23: 0.8913 REMARK 3 S31: -0.3675 S32: 0.0591 S33: 0.0632 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 2 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.7524 13.1415 -18.5934 REMARK 3 T TENSOR REMARK 3 T11: 0.6357 T22: 0.3196 REMARK 3 T33: 0.4703 T12: 0.1315 REMARK 3 T13: -0.1419 T23: -0.0434 REMARK 3 L TENSOR REMARK 3 L11: 3.9142 L22: 2.8152 REMARK 3 L33: 9.1411 L12: -0.3989 REMARK 3 L13: 1.9280 L23: -3.2142 REMARK 3 S TENSOR REMARK 3 S11: 0.2641 S12: 0.0378 S13: -0.1781 REMARK 3 S21: -0.2603 S22: 0.1037 S23: 0.7216 REMARK 3 S31: 0.2431 S32: -0.2611 S33: -0.2803 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 5DEU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000213077. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97931 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50752 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.82800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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: 4NM6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 26% PEGMME2000,0.1M MES6.4, PH 6.4, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 130.43200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 130.43200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 24.13100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.76100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 24.13100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.76100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 130.43200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 24.13100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 43.76100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 130.43200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 24.13100 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 43.76100 REMARK 290 SMTRY3 8 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 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 1127 REMARK 465 SER A 1128 REMARK 465 ASP A 1129 REMARK 465 PHE A 1130 REMARK 465 PRO A 1131 REMARK 465 ARG A 1813 REMARK 465 GLN A 1814 REMARK 465 ARG A 1815 REMARK 465 LYS A 1816 REMARK 465 LEU A 1817 REMARK 465 GLU A 1818 REMARK 465 ALA A 1819 REMARK 465 LYS A 1820 REMARK 465 LYS A 1821 REMARK 465 ALA A 1822 REMARK 465 ALA A 1823 REMARK 465 ALA A 1824 REMARK 465 GLU A 1825 REMARK 465 LYS A 1826 REMARK 465 LEU A 1827 REMARK 465 SER A 1828 REMARK 465 GLY A 1829 REMARK 465 GLY A 1830 REMARK 465 GLY A 1831 REMARK 465 GLY A 1832 REMARK 465 SER A 1833 REMARK 465 GLY A 1834 REMARK 465 GLY A 1835 REMARK 465 GLY A 1836 REMARK 465 GLY A 1837 REMARK 465 SER A 1838 REMARK 465 GLY A 1839 REMARK 465 GLY A 1840 REMARK 465 GLY A 1841 REMARK 465 ALA A 1922 REMARK 465 GLU A 1923 REMARK 465 LYS A 1924 REMARK 465 ALA A 1925 REMARK 465 ARG A 1926 REMARK 465 GLU A 1927 REMARK 465 LYS A 1928 REMARK 465 GLU A 1929 REMARK 465 GLU A 1930 REMARK 465 GLU A 1931 REMARK 465 CYS A 1932 REMARK 465 GLU A 1933 REMARK 465 LYS A 1934 REMARK 465 TYR A 1935 REMARK 465 GLY A 1936 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DA B 4 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG C 8 O4' - C1' - N9 ANGL. DEV. = -5.4 DEGREES REMARK 500 DT C 9 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT C 12 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES 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 GLU A1234 78.00 -103.74 REMARK 500 HIS A1893 67.02 -160.98 REMARK 500 MET A1907 43.52 -107.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A2004 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1133 SG REMARK 620 2 CYS A1135 SG 107.5 REMARK 620 3 HIS A1219 ND1 102.8 106.1 REMARK 620 4 CYS A1221 SG 112.0 107.5 120.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A2005 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1193 SG REMARK 620 2 CYS A1271 SG 116.7 REMARK 620 3 CYS A1273 SG 102.6 114.4 REMARK 620 4 HIS A1380 NE2 111.1 93.8 118.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A2006 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1289 SG REMARK 620 2 CYS A1298 SG 108.0 REMARK 620 3 CYS A1358 SG 119.2 112.4 REMARK 620 4 HIS A1912 ND1 105.1 106.9 104.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A2003 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A1382 NE2 REMARK 620 2 ASP A1384 OD2 115.0 REMARK 620 3 HIS A1881 NE2 94.1 98.1 REMARK 620 4 OGA A2001 O1 91.4 99.5 157.2 REMARK 620 5 OGA A2001 O2' 98.0 146.9 81.1 76.3 REMARK 620 6 HOH A2113 O 174.3 67.4 90.6 83.0 79.5 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 OGA A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES A 2002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE A 2003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 2004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 2005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 2006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 2007 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5D9Y RELATED DB: PDB DBREF 5DEU A 1129 1828 UNP Q6N021 TET2_HUMAN 1129 1480 DBREF 5DEU A 1844 1935 UNP Q6N021 TET2_HUMAN 1844 1935 DBREF 5DEU B 1 12 PDB 5DEU 5DEU 1 12 DBREF 5DEU C 2 12 PDB 5DEU 5DEU 2 12 SEQADV 5DEU GLY A 1127 UNP Q6N021 EXPRESSION TAG SEQADV 5DEU SER A 1128 UNP Q6N021 EXPRESSION TAG SEQADV 5DEU GLY A 1829 UNP Q6N021 LINKER SEQADV 5DEU GLY A 1830 UNP Q6N021 LINKER SEQADV 5DEU GLY A 1831 UNP Q6N021 LINKER SEQADV 5DEU GLY A 1832 UNP Q6N021 LINKER SEQADV 5DEU SER A 1833 UNP Q6N021 LINKER SEQADV 5DEU GLY A 1834 UNP Q6N021 LINKER SEQADV 5DEU GLY A 1835 UNP Q6N021 LINKER SEQADV 5DEU GLY A 1836 UNP Q6N021 LINKER SEQADV 5DEU GLY A 1837 UNP Q6N021 LINKER SEQADV 5DEU SER A 1838 UNP Q6N021 LINKER SEQADV 5DEU GLY A 1839 UNP Q6N021 LINKER SEQADV 5DEU GLY A 1840 UNP Q6N021 LINKER SEQADV 5DEU GLY A 1841 UNP Q6N021 LINKER SEQADV 5DEU GLY A 1842 UNP Q6N021 LINKER SEQADV 5DEU SER A 1843 UNP Q6N021 LINKER SEQADV 5DEU GLY A 1936 UNP Q6N021 EXPRESSION TAG SEQRES 1 A 462 GLY SER ASP PHE PRO SER CYS ARG CYS VAL GLU GLN ILE SEQRES 2 A 462 ILE GLU LYS ASP GLU GLY PRO PHE TYR THR HIS LEU GLY SEQRES 3 A 462 ALA GLY PRO ASN VAL ALA ALA ILE ARG GLU ILE MET GLU SEQRES 4 A 462 GLU ARG PHE GLY GLN LYS GLY LYS ALA ILE ARG ILE GLU SEQRES 5 A 462 ARG VAL ILE TYR THR GLY LYS GLU GLY LYS SER SER GLN SEQRES 6 A 462 GLY CYS PRO ILE ALA LYS TRP VAL VAL ARG ARG SER SER SEQRES 7 A 462 SER GLU GLU LYS LEU LEU CYS LEU VAL ARG GLU ARG ALA SEQRES 8 A 462 GLY HIS THR CYS GLU ALA ALA VAL ILE VAL ILE LEU ILE SEQRES 9 A 462 LEU VAL TRP GLU GLY ILE PRO LEU SER LEU ALA ASP LYS SEQRES 10 A 462 LEU TYR SER GLU LEU THR GLU THR LEU ARG LYS TYR GLY SEQRES 11 A 462 THR LEU THR ASN ARG ARG CYS ALA LEU ASN GLU GLU ARG SEQRES 12 A 462 THR CYS ALA CYS GLN GLY LEU ASP PRO GLU THR CYS GLY SEQRES 13 A 462 ALA SER PHE SER PHE GLY CYS SER TRP SER MET TYR TYR SEQRES 14 A 462 ASN GLY CYS LYS PHE ALA ARG SER LYS ILE PRO ARG LYS SEQRES 15 A 462 PHE LYS LEU LEU GLY ASP ASP PRO LYS GLU GLU GLU LYS SEQRES 16 A 462 LEU GLU SER HIS LEU GLN ASN LEU SER THR LEU MET ALA SEQRES 17 A 462 PRO THR TYR LYS LYS LEU ALA PRO ASP ALA TYR ASN ASN SEQRES 18 A 462 GLN ILE GLU TYR GLU HIS ARG ALA PRO GLU CYS ARG LEU SEQRES 19 A 462 GLY LEU LYS GLU GLY ARG PRO PHE SER GLY VAL THR ALA SEQRES 20 A 462 CYS LEU ASP PHE CYS ALA HIS ALA HIS ARG ASP LEU HIS SEQRES 21 A 462 ASN MET GLN ASN GLY SER THR LEU VAL CYS THR LEU THR SEQRES 22 A 462 ARG GLU ASP ASN ARG GLU PHE GLY GLY LYS PRO GLU ASP SEQRES 23 A 462 GLU GLN LEU HIS VAL LEU PRO LEU TYR LYS VAL SER ASP SEQRES 24 A 462 VAL ASP GLU PHE GLY SER VAL GLU ALA GLN GLU GLU LYS SEQRES 25 A 462 LYS ARG SER GLY ALA ILE GLN VAL LEU SER SER PHE ARG SEQRES 26 A 462 ARG LYS VAL ARG MET LEU ALA GLU PRO VAL LYS THR CYS SEQRES 27 A 462 ARG GLN ARG LYS LEU GLU ALA LYS LYS ALA ALA ALA GLU SEQRES 28 A 462 LYS LEU SER GLY GLY GLY GLY SER GLY GLY GLY GLY SER SEQRES 29 A 462 GLY GLY GLY GLY SER ASP GLU VAL TRP SER ASP SER GLU SEQRES 30 A 462 GLN SER PHE LEU ASP PRO ASP ILE GLY GLY VAL ALA VAL SEQRES 31 A 462 ALA PRO THR HIS GLY SER ILE LEU ILE GLU CYS ALA LYS SEQRES 32 A 462 ARG GLU LEU HIS ALA THR THR PRO LEU LYS ASN PRO ASN SEQRES 33 A 462 ARG ASN HIS PRO THR ARG ILE SER LEU VAL PHE TYR GLN SEQRES 34 A 462 HIS LYS SER MET ASN GLU PRO LYS HIS GLY LEU ALA LEU SEQRES 35 A 462 TRP GLU ALA LYS MET ALA GLU LYS ALA ARG GLU LYS GLU SEQRES 36 A 462 GLU GLU CYS GLU LYS TYR GLY SEQRES 1 B 12 DA DC DC DA DC 5HC DG DG DT DG DG DT SEQRES 1 C 11 DC DC DA DC 5HC DG DG DT DG DG DT HET 5HC B 6 21 HET 5HC C 6 21 HET OGA A2001 10 HET MES A2002 12 HET FE A2003 1 HET ZN A2004 1 HET ZN A2005 1 HET ZN A2006 1 HET CL A2007 1 HETNAM 5HC 2'-DEOXY-5-(HYDROXYMETHYL)CYTIDINE 5'-(DIHYDROGEN HETNAM 2 5HC PHOSPHATE) HETNAM OGA N-OXALYLGLYCINE HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM FE FE (III) ION HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION FORMUL 2 5HC 2(C10 H16 N3 O8 P) FORMUL 4 OGA C4 H5 N O5 FORMUL 5 MES C6 H13 N O4 S FORMUL 6 FE FE 3+ FORMUL 7 ZN 3(ZN 2+) FORMUL 10 CL CL 1- FORMUL 11 HOH *309(H2 O) HELIX 1 AA1 ILE A 1140 GLY A 1145 1 6 HELIX 2 AA2 ASN A 1156 GLY A 1169 1 14 HELIX 3 AA3 LYS A 1171 LYS A 1173 5 3 HELIX 4 AA4 PRO A 1237 GLY A 1256 1 20 HELIX 5 AA5 ARG A 1261 LEU A 1265 5 5 HELIX 6 AA6 ASP A 1315 ALA A 1341 1 27 HELIX 7 AA7 ALA A 1341 ILE A 1349 1 9 HELIX 8 AA8 ALA A 1355 ARG A 1359 5 5 HELIX 9 AA9 SER A 1431 SER A 1441 1 11 HELIX 10 AB1 SER A 1850 ASP A 1856 1 7 HELIX 11 AB2 GLU A 1909 HIS A 1912 5 4 HELIX 12 AB3 GLY A 1913 MET A 1921 1 9 SHEET 1 AA1 7 ALA A1153 GLY A1154 0 SHEET 2 AA1 7 VAL A1225 VAL A1232 -1 O VAL A1225 N GLY A1154 SHEET 3 AA1 7 ILE A1871 GLU A1874 -1 O ILE A1873 N ILE A1230 SHEET 4 AA1 7 THR A1393 THR A1399 -1 N THR A1393 O GLU A1874 SHEET 5 AA1 7 ARG A1896 TYR A1902 -1 O PHE A1901 N LEU A1394 SHEET 6 AA1 7 GLY A1370 LEU A1375 -1 N THR A1372 O VAL A1900 SHEET 7 AA1 7 ALA A1283 GLY A1288 -1 N PHE A1287 O VAL A1371 SHEET 1 AA2 5 ALA A1153 GLY A1154 0 SHEET 2 AA2 5 VAL A1225 VAL A1232 -1 O VAL A1225 N GLY A1154 SHEET 3 AA2 5 LEU A1209 GLU A1215 -1 N LEU A1210 O LEU A1231 SHEET 4 AA2 5 ILE A1175 TYR A1182 1 N ARG A1176 O LEU A1209 SHEET 5 AA2 5 TYR A1421 VAL A1423 -1 O LYS A1422 N ILE A1181 SHEET 1 AA3 5 ILE A1444 VAL A1446 0 SHEET 2 AA3 5 TRP A1198 VAL A1200 -1 N VAL A1199 O GLN A1445 SHEET 3 AA3 5 VAL A1862 VAL A1864 1 O ALA A1863 N VAL A1200 SHEET 4 AA3 5 HIS A1416 LEU A1418 -1 N LEU A1418 O VAL A1862 SHEET 5 AA3 5 ALA A1882 THR A1883 -1 O ALA A1882 N VAL A1417 SHEET 1 AA4 2 TRP A1291 SER A1292 0 SHEET 2 AA4 2 GLY A1297 CYS A1298 -1 O GLY A1297 N SER A1292 SHEET 1 AA5 2 ARG A1451 LEU A1457 0 SHEET 2 AA5 2 SER A1843 ASP A1849 -1 O VAL A1846 N VAL A1454 LINK O3' DC B 5 P 5HC B 6 1555 1555 1.61 LINK O3' 5HC B 6 P DG B 7 1555 1555 1.60 LINK O3' DC C 5 P 5HC C 6 1555 1555 1.61 LINK O3' 5HC C 6 P DG C 7 1555 1555 1.61 LINK SG CYS A1133 ZN ZN A2004 1555 1555 2.32 LINK SG CYS A1135 ZN ZN A2004 1555 1555 2.38 LINK SG CYS A1193 ZN ZN A2005 1555 1555 2.44 LINK ND1 HIS A1219 ZN ZN A2004 1555 1555 2.08 LINK SG CYS A1221 ZN ZN A2004 1555 1555 2.38 LINK SG CYS A1271 ZN ZN A2005 1555 1555 2.43 LINK SG CYS A1273 ZN ZN A2005 1555 1555 2.31 LINK SG CYS A1289 ZN ZN A2006 1555 1555 2.35 LINK SG CYS A1298 ZN ZN A2006 1555 1555 2.34 LINK SG CYS A1358 ZN ZN A2006 1555 1555 2.36 LINK NE2 HIS A1380 ZN ZN A2005 1555 1555 2.05 LINK NE2 HIS A1382 FE FE A2003 1555 1555 2.13 LINK OD2 ASP A1384 FE FE A2003 1555 1555 2.16 LINK NE2 HIS A1881 FE FE A2003 1555 1555 2.08 LINK ND1 HIS A1912 ZN ZN A2006 1555 1555 2.20 LINK O1 OGA A2001 FE FE A2003 1555 1555 2.17 LINK O2' OGA A2001 FE FE A2003 1555 1555 2.23 LINK FE FE A2003 O HOH A2113 1555 1555 2.20 CISPEP 1 SER A 1132 CYS A 1133 0 13.42 SITE 1 AC1 12 ARG A1261 CYS A1374 HIS A1382 ASP A1384 SITE 2 AC1 12 HIS A1416 HIS A1881 THR A1883 ARG A1896 SITE 3 AC1 12 SER A1898 FE A2003 HOH A2113 5HC B 6 SITE 1 AC2 8 GLU A1186 ALA A1381 HIS A1382 ARG A1383 SITE 2 AC2 8 LEU A1385 LEU A1880 HOH A2111 DG C 11 SITE 1 AC3 5 HIS A1382 ASP A1384 HIS A1881 OGA A2001 SITE 2 AC3 5 HOH A2113 SITE 1 AC4 4 CYS A1133 CYS A1135 HIS A1219 CYS A1221 SITE 1 AC5 4 CYS A1193 CYS A1271 CYS A1273 HIS A1380 SITE 1 AC6 4 CYS A1289 CYS A1298 CYS A1358 HIS A1912 SITE 1 AC7 5 ASN A1387 SER A1392 THR A1393 ALA A1876 SITE 2 AC7 5 LYS A1877 CRYST1 48.262 87.522 260.864 90.00 90.00 90.00 C 2 2 21 8 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 0.020720 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011426 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003833 0.00000