HEADER OXIDOREDUCTASE 03-FEB-21 7NE6 TITLE HUMAN TET2 IN COMPLEX WITH UNFAVOURABLE DNA SUBSTRATE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYLCYTOSINE DIOXYGENASE TET2; COMPND 3 CHAIN: A; COMPND 4 EC: 1.14.11.-,1.14.11.-; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: OXYGENASE DOMAIN OF THE 2OGFEDO SUPERFAMILY,OXYGENASE COMPND 7 DOMAIN OF THE 2OGFEDO SUPERFAMILY,OXYGENASE DOMAIN OF THE 2OGFEDO COMPND 8 SUPERFAMILY,OXYGENASE DOMAIN OF THE 2OGFEDO SUPERFAMILY; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(*AP*CP*AP*GP*GP*(5CM)P*GP*CP*CP*TP*G)-3'); COMPND 11 CHAIN: B, C; COMPND 12 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 EXPRESSION_SYSTEM_STRAIN: BL RIL; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630 KEYWDS DNA BINDING, COMPLEX, IRON DEPENDENT DIOXYGENASE, TET2, DNA KEYWDS 2 MODIFICATION, EPIGENETICS, 5-METHYLCYTOSINE, ION BINDING, IRON KEYWDS 3 BINDING PROTEIN, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR D.RAFALSKI,M.BOCHTLER REVDAT 5 31-JAN-24 7NE6 1 REMARK REVDAT 4 21-SEP-22 7NE6 1 JRNL REVDAT 3 24-AUG-22 7NE6 1 COMPND SOURCE DBREF SEQADV REVDAT 2 11-MAY-22 7NE6 1 REMARK REVDAT 1 02-MAR-22 7NE6 0 JRNL AUTH M.RAVICHANDRAN,D.RAFALSKI,C.I.DAVIES,O.ORTEGA-RECALDE,X.NAN, JRNL AUTH 2 C.R.GLANFIELD,A.KOTTER,K.MISZTAL,A.H.WANG,M.WOJCIECHOWSKI, JRNL AUTH 3 M.RAZEW,I.M.MAYYAS,O.KARDAILSKY,U.SCHWARTZ,K.ZEMBRZYCKI, JRNL AUTH 4 I.M.MORISON,M.HELM,D.WEICHENHAN,R.Z.JURKOWSKA,F.KRUEGER, JRNL AUTH 5 C.PLASS,M.ZACHARIAS,M.BOCHTLER,T.A.HORE,T.P.JURKOWSKI JRNL TITL PRONOUNCED SEQUENCE SPECIFICITY OF THE TET ENZYME CATALYTIC JRNL TITL 2 DOMAIN GUIDES ITS CELLULAR FUNCTION. JRNL REF SCI ADV V. 8 M2427 2022 JRNL REFN ESSN 2375-2548 JRNL PMID 36070377 JRNL DOI 10.1126/SCIADV.ABM2427 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 24976 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1250 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 43.9700 - 4.7800 1.00 2819 149 0.1768 0.2092 REMARK 3 2 4.7800 - 3.8000 1.00 2692 142 0.1589 0.1728 REMARK 3 3 3.8000 - 3.3200 1.00 2669 140 0.1768 0.2119 REMARK 3 4 3.3200 - 3.0100 1.00 2634 139 0.2028 0.2460 REMARK 3 5 3.0100 - 2.8000 1.00 2619 138 0.2214 0.2557 REMARK 3 6 2.8000 - 2.6300 1.00 2614 137 0.2451 0.3210 REMARK 3 7 2.6300 - 2.5000 1.00 2627 138 0.2572 0.3006 REMARK 3 8 2.5000 - 2.3900 0.99 2584 137 0.2590 0.2814 REMARK 3 9 2.3900 - 2.3000 0.93 2468 130 0.2820 0.2821 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) : 0.235 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.945 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.38 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.61 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 : 0.003 3844 REMARK 3 ANGLE : 0.571 5294 REMARK 3 CHIRALITY : 0.042 576 REMARK 3 PLANARITY : 0.003 613 REMARK 3 DIHEDRAL : 10.725 2989 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 1132 THROUGH 1930) REMARK 3 ORIGIN FOR THE GROUP (A): 16.1268 0.1575 -36.4193 REMARK 3 T TENSOR REMARK 3 T11: 0.2217 T22: 0.1893 REMARK 3 T33: 0.2863 T12: 0.0302 REMARK 3 T13: -0.0811 T23: 0.0008 REMARK 3 L TENSOR REMARK 3 L11: 1.8355 L22: 2.2403 REMARK 3 L33: 2.9267 L12: -0.0480 REMARK 3 L13: -0.3493 L23: 0.1320 REMARK 3 S TENSOR REMARK 3 S11: -0.0493 S12: -0.0106 S13: -0.0508 REMARK 3 S21: 0.0435 S22: -0.0022 S23: 0.1837 REMARK 3 S31: -0.1984 S32: -0.1148 S33: 0.0490 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 1 THROUGH 11) REMARK 3 ORIGIN FOR THE GROUP (A): 5.2365 9.3929 -17.8288 REMARK 3 T TENSOR REMARK 3 T11: 0.5465 T22: 0.3888 REMARK 3 T33: 0.4084 T12: 0.0189 REMARK 3 T13: -0.0311 T23: 0.0459 REMARK 3 L TENSOR REMARK 3 L11: 3.2047 L22: 3.6645 REMARK 3 L33: 3.8254 L12: -0.9220 REMARK 3 L13: -0.1665 L23: -0.2824 REMARK 3 S TENSOR REMARK 3 S11: 0.0442 S12: -0.5328 S13: 0.0813 REMARK 3 S21: 0.6198 S22: 0.0908 S23: 0.4443 REMARK 3 S31: -0.4995 S32: -0.2072 S33: -0.1342 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'C' AND RESID 1 THROUGH 12) REMARK 3 ORIGIN FOR THE GROUP (A): 4.0059 11.2181 -16.8517 REMARK 3 T TENSOR REMARK 3 T11: 0.7964 T22: 0.5874 REMARK 3 T33: 0.4612 T12: 0.2213 REMARK 3 T13: 0.0761 T23: 0.0548 REMARK 3 L TENSOR REMARK 3 L11: 2.8694 L22: 4.0219 REMARK 3 L33: 6.8168 L12: -0.0835 REMARK 3 L13: 0.3537 L23: -0.9580 REMARK 3 S TENSOR REMARK 3 S11: 0.0637 S12: -0.4558 S13: -0.2800 REMARK 3 S21: 0.8980 S22: 0.0947 S23: 0.6547 REMARK 3 S31: -0.4932 S32: -0.2555 S33: -0.1583 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 7NE6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1292113777. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-APR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24979 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 43.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.11690 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.84630 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 4NM6 REMARK 200 REMARK 200 REMARK: UNIT CELL: (47.858, 87.943, 261.988, 90, 90, 90) REMARK 200 SPACE GROUP: C 2 2 21 (NO. 20) REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES PH=6.3, 23% PEG2000MME, PH REMARK 280 6.3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 278K 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 130.99400 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 130.99400 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 23.92900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.97150 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 23.92900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.97150 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 130.99400 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 23.92900 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 43.97150 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 130.99400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 23.92900 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 43.97150 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: 5830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 5.0 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 1126 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 VAL A 1136 REMARK 465 GLU A 1137 REMARK 465 GLN A 1138 REMARK 465 ILE A 1139 REMARK 465 ILE A 1140 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 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 465 DT B 12 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 ARG A1134 CG CD NE CZ NH1 NH2 REMARK 470 GLU A1141 CG CD OE1 OE2 REMARK 470 LYS A1304 CG CD CE NZ REMARK 470 ILE A1305 CG1 CG2 CD1 REMARK 470 ASP A1314 CG OD1 OD2 REMARK 470 LYS A1317 CG CD CE NZ REMARK 470 GLU A1320 CG CD OE1 OE2 REMARK 470 LYS A1409 CG CD CE NZ REMARK 470 ARG A1452 CG CD NE CZ NH1 NH2 REMARK 470 LYS A1453 CG CD CE NZ REMARK 470 LYS A1462 CG CD CE NZ REMARK 470 ARG A1465 CG CD NE CZ NH1 NH2 REMARK 470 VAL A1846 CG1 CG2 REMARK 470 LYS A1911 CG CD CE NZ REMARK 470 LYS A1920 CG CD CE NZ REMARK 470 LYS A1924 CG CD CE NZ REMARK 470 ARG A1926 CG CD NE CZ NH1 NH2 REMARK 470 GLU A1927 CG CD OE1 OE2 REMARK 470 LYS A1928 CG CD CE NZ REMARK 470 GLU A1929 CG CD OE1 OE2 REMARK 470 GLU A1930 CG 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 LYS A1142 -90.15 -139.12 REMARK 500 GLU A1234 75.77 -100.60 REMARK 500 ALA A1272 29.02 -143.54 REMARK 500 ILE A1305 75.98 57.44 REMARK 500 THR A1463 -70.50 -48.74 REMARK 500 HIS A1893 70.60 -156.57 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 A2002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1133 SG REMARK 620 2 CYS A1135 SG 112.9 REMARK 620 3 HIS A1219 ND1 105.6 114.4 REMARK 620 4 CYS A1221 SG 104.3 111.4 107.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A2001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1193 SG REMARK 620 2 CYS A1271 SG 128.8 REMARK 620 3 CYS A1273 SG 94.9 110.5 REMARK 620 4 HIS A1380 NE2 114.2 91.0 119.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A2003 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1289 SG REMARK 620 2 CYS A1298 SG 110.5 REMARK 620 3 CYS A1358 SG 114.6 114.9 REMARK 620 4 HIS A1912 ND1 105.0 107.7 103.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A2007 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A1382 NE2 REMARK 620 2 ASP A1384 OD1 80.0 REMARK 620 3 ASP A1384 OD2 127.0 48.2 REMARK 620 4 HIS A1881 NE2 99.9 113.2 92.1 REMARK 620 5 OGA A2004 O1 84.9 84.8 98.9 161.9 REMARK 620 6 OGA A2004 O2' 99.6 155.8 131.9 90.8 71.1 REMARK 620 7 HOH A2189 O 167.9 108.1 63.2 85.2 86.9 69.3 REMARK 620 N 1 2 3 4 5 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NM6 RELATED DB: PDB REMARK 900 TET2 IN COMPLEX WITH DNA OLIGO DBREF 7NE6 A 1129 1828 UNP Q6N021 TET2_HUMAN 1129 1480 DBREF 7NE6 A 1844 1936 UNP Q6N021 TET2_HUMAN 1844 1936 DBREF 7NE6 B 1 12 PDB 7NE6 7NE6 1 12 DBREF 7NE6 C 1 12 PDB 7NE6 7NE6 1 12 SEQADV 7NE6 GLY A 1126 UNP Q6N021 EXPRESSION TAG SEQADV 7NE6 GLY A 1127 UNP Q6N021 EXPRESSION TAG SEQADV 7NE6 SER A 1128 UNP Q6N021 EXPRESSION TAG SEQADV 7NE6 GLY A 1829 UNP Q6N021 LINKER SEQADV 7NE6 GLY A 1830 UNP Q6N021 LINKER SEQADV 7NE6 GLY A 1831 UNP Q6N021 LINKER SEQADV 7NE6 GLY A 1832 UNP Q6N021 LINKER SEQADV 7NE6 SER A 1833 UNP Q6N021 LINKER SEQADV 7NE6 GLY A 1834 UNP Q6N021 LINKER SEQADV 7NE6 GLY A 1835 UNP Q6N021 LINKER SEQADV 7NE6 GLY A 1836 UNP Q6N021 LINKER SEQADV 7NE6 GLY A 1837 UNP Q6N021 LINKER SEQADV 7NE6 SER A 1838 UNP Q6N021 LINKER SEQADV 7NE6 GLY A 1839 UNP Q6N021 LINKER SEQADV 7NE6 GLY A 1840 UNP Q6N021 LINKER SEQADV 7NE6 GLY A 1841 UNP Q6N021 LINKER SEQADV 7NE6 GLY A 1842 UNP Q6N021 LINKER SEQADV 7NE6 SER A 1843 UNP Q6N021 LINKER SEQRES 1 A 463 GLY GLY SER ASP PHE PRO SER CYS ARG CYS VAL GLU GLN SEQRES 2 A 463 ILE ILE GLU LYS ASP GLU GLY PRO PHE TYR THR HIS LEU SEQRES 3 A 463 GLY ALA GLY PRO ASN VAL ALA ALA ILE ARG GLU ILE MET SEQRES 4 A 463 GLU GLU ARG PHE GLY GLN LYS GLY LYS ALA ILE ARG ILE SEQRES 5 A 463 GLU ARG VAL ILE TYR THR GLY LYS GLU GLY LYS SER SER SEQRES 6 A 463 GLN GLY CYS PRO ILE ALA LYS TRP VAL VAL ARG ARG SER SEQRES 7 A 463 SER SER GLU GLU LYS LEU LEU CYS LEU VAL ARG GLU ARG SEQRES 8 A 463 ALA GLY HIS THR CYS GLU ALA ALA VAL ILE VAL ILE LEU SEQRES 9 A 463 ILE LEU VAL TRP GLU GLY ILE PRO LEU SER LEU ALA ASP SEQRES 10 A 463 LYS LEU TYR SER GLU LEU THR GLU THR LEU ARG LYS TYR SEQRES 11 A 463 GLY THR LEU THR ASN ARG ARG CYS ALA LEU ASN GLU GLU SEQRES 12 A 463 ARG THR CYS ALA CYS GLN GLY LEU ASP PRO GLU THR CYS SEQRES 13 A 463 GLY ALA SER PHE SER PHE GLY CYS SER TRP SER MET TYR SEQRES 14 A 463 TYR ASN GLY CYS LYS PHE ALA ARG SER LYS ILE PRO ARG SEQRES 15 A 463 LYS PHE LYS LEU LEU GLY ASP ASP PRO LYS GLU GLU GLU SEQRES 16 A 463 LYS LEU GLU SER HIS LEU GLN ASN LEU SER THR LEU MET SEQRES 17 A 463 ALA PRO THR TYR LYS LYS LEU ALA PRO ASP ALA TYR ASN SEQRES 18 A 463 ASN GLN ILE GLU TYR GLU HIS ARG ALA PRO GLU CYS ARG SEQRES 19 A 463 LEU GLY LEU LYS GLU GLY ARG PRO PHE SER GLY VAL THR SEQRES 20 A 463 ALA CYS LEU ASP PHE CYS ALA HIS ALA HIS ARG ASP LEU SEQRES 21 A 463 HIS ASN MET GLN ASN GLY SER THR LEU VAL CYS THR LEU SEQRES 22 A 463 THR ARG GLU ASP ASN ARG GLU PHE GLY GLY LYS PRO GLU SEQRES 23 A 463 ASP GLU GLN LEU HIS VAL LEU PRO LEU TYR LYS VAL SER SEQRES 24 A 463 ASP VAL ASP GLU PHE GLY SER VAL GLU ALA GLN GLU GLU SEQRES 25 A 463 LYS LYS ARG SER GLY ALA ILE GLN VAL LEU SER SER PHE SEQRES 26 A 463 ARG ARG LYS VAL ARG MET LEU ALA GLU PRO VAL LYS THR SEQRES 27 A 463 CYS ARG GLN ARG LYS LEU GLU ALA LYS LYS ALA ALA ALA SEQRES 28 A 463 GLU LYS LEU SER GLY GLY GLY GLY SER GLY GLY GLY GLY SEQRES 29 A 463 SER GLY GLY GLY GLY SER ASP GLU VAL TRP SER ASP SER SEQRES 30 A 463 GLU GLN SER PHE LEU ASP PRO ASP ILE GLY GLY VAL ALA SEQRES 31 A 463 VAL ALA PRO THR HIS GLY SER ILE LEU ILE GLU CYS ALA SEQRES 32 A 463 LYS ARG GLU LEU HIS ALA THR THR PRO LEU LYS ASN PRO SEQRES 33 A 463 ASN ARG ASN HIS PRO THR ARG ILE SER LEU VAL PHE TYR SEQRES 34 A 463 GLN HIS LYS SER MET ASN GLU PRO LYS HIS GLY LEU ALA SEQRES 35 A 463 LEU TRP GLU ALA LYS MET ALA GLU LYS ALA ARG GLU LYS SEQRES 36 A 463 GLU GLU GLU CYS GLU LYS TYR GLY SEQRES 1 B 12 DA DC DA DG DG 5CM DG DC DC DT DG DT SEQRES 1 C 12 DA DC DA DG DG 5CM DG DC DC DT DG DT HET 5CM B 6 20 HET 5CM C 6 20 HET ZN A2001 1 HET ZN A2002 1 HET ZN A2003 1 HET OGA A2004 10 HET EDO A2005 4 HET MES A2006 12 HET MN A2007 1 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM ZN ZINC ION HETNAM OGA N-OXALYLGLYCINE HETNAM EDO 1,2-ETHANEDIOL HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM MN MANGANESE (II) ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 5CM 2(C10 H16 N3 O7 P) FORMUL 4 ZN 3(ZN 2+) FORMUL 7 OGA C4 H5 N O5 FORMUL 8 EDO C2 H6 O2 FORMUL 9 MES C6 H13 N O4 S FORMUL 10 MN MN 2+ FORMUL 11 HOH *313(H2 O) HELIX 1 AA1 ASN A 1156 GLY A 1169 1 14 HELIX 2 AA2 LYS A 1171 LYS A 1173 5 3 HELIX 3 AA3 PRO A 1237 GLY A 1256 1 20 HELIX 4 AA4 ARG A 1261 LEU A 1265 5 5 HELIX 5 AA5 ASP A 1315 ALA A 1341 1 27 HELIX 6 AA6 ALA A 1341 ILE A 1349 1 9 HELIX 7 AA7 ALA A 1355 ARG A 1359 5 5 HELIX 8 AA8 SER A 1431 GLY A 1442 1 12 HELIX 9 AA9 SER A 1850 ASP A 1856 1 7 HELIX 10 AB1 GLU A 1909 HIS A 1912 5 4 HELIX 11 AB2 GLY A 1913 GLU A 1929 1 17 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 ILE A1897 N LEU A1398 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 A1285 O ALA A1373 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 A1212 O ILE A1228 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' DG B 5 P 5CM B 6 1555 1555 1.60 LINK O3' 5CM B 6 P DG B 7 1555 1555 1.61 LINK O3' DG C 5 P 5CM C 6 1555 1555 1.61 LINK O3' 5CM C 6 P DG C 7 1555 1555 1.61 LINK SG CYS A1133 ZN ZN A2002 1555 1555 2.51 LINK SG CYS A1135 ZN ZN A2002 1555 1555 2.46 LINK SG CYS A1193 ZN ZN A2001 1555 1555 2.37 LINK ND1 HIS A1219 ZN ZN A2002 1555 1555 2.01 LINK SG CYS A1221 ZN ZN A2002 1555 1555 2.38 LINK SG CYS A1271 ZN ZN A2001 1555 1555 2.42 LINK SG CYS A1273 ZN ZN A2001 1555 1555 2.32 LINK SG CYS A1289 ZN ZN A2003 1555 1555 2.64 LINK SG CYS A1298 ZN ZN A2003 1555 1555 2.31 LINK SG CYS A1358 ZN ZN A2003 1555 1555 2.34 LINK NE2 HIS A1380 ZN ZN A2001 1555 1555 2.14 LINK NE2 HIS A1382 MN MN A2007 1555 1555 2.38 LINK OD1 ASP A1384 MN MN A2007 1555 1555 2.76 LINK OD2 ASP A1384 MN MN A2007 1555 1555 2.58 LINK NE2 HIS A1881 MN MN A2007 1555 1555 2.39 LINK ND1 HIS A1912 ZN ZN A2003 1555 1555 2.08 LINK O1 OGA A2004 MN MN A2007 1555 1555 2.47 LINK O2' OGA A2004 MN MN A2007 1555 1555 2.14 LINK MN MN A2007 O HOH A2189 1555 1555 2.55 CRYST1 47.858 87.943 261.988 90.00 90.00 90.00 C 2 2 21 16 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 0.020895 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011371 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003817 0.00000