HEADER OXIDOREDUCTASE 03-FEB-21 7NE3 TITLE HUMAN TET2 IN COMPLEX WITH FAVOURABLE 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 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*AP*CP*AP*GP*GP*(5CM)P*GP*CP*CP*TP*G)-3'); COMPND 9 CHAIN: B, C; COMPND 10 ENGINEERED: YES; COMPND 11 MUTATION: 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 7NE3 1 REMARK REVDAT 4 22-NOV-23 7NE3 1 REMARK REVDAT 3 21-SEP-22 7NE3 1 JRNL REVDAT 2 24-AUG-22 7NE3 1 COMPND SOURCE DBREF SEQADV REVDAT 1 02-MAR-22 7NE3 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. 2.26 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) : 2.26 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 26439 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1322 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 43.8600 - 4.6900 1.00 2962 156 0.1686 0.1990 REMARK 3 2 4.6900 - 3.7300 1.00 2834 150 0.1431 0.2007 REMARK 3 3 3.7300 - 3.2600 1.00 2792 147 0.1600 0.2079 REMARK 3 4 3.2600 - 2.9600 1.00 2773 145 0.1829 0.2531 REMARK 3 5 2.9600 - 2.7500 1.00 2777 147 0.1933 0.2525 REMARK 3 6 2.7500 - 2.5800 1.00 2764 145 0.2101 0.2910 REMARK 3 7 2.5800 - 2.4500 1.00 2752 145 0.2308 0.3078 REMARK 3 8 2.4500 - 2.3500 1.00 2743 144 0.2503 0.3037 REMARK 3 9 2.3500 - 2.2600 0.99 2720 143 0.2689 0.3326 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) : 0.319 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.468 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 51.69 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.02 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 3824 REMARK 3 ANGLE : 0.911 5267 REMARK 3 CHIRALITY : 0.054 575 REMARK 3 PLANARITY : 0.005 609 REMARK 3 DIHEDRAL : 10.998 2959 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 1925) REMARK 3 ORIGIN FOR THE GROUP (A): 16.0903 0.4806 -36.4953 REMARK 3 T TENSOR REMARK 3 T11: 0.3265 T22: 0.3265 REMARK 3 T33: 0.4137 T12: 0.0086 REMARK 3 T13: -0.0715 T23: 0.0222 REMARK 3 L TENSOR REMARK 3 L11: 1.6520 L22: 1.8951 REMARK 3 L33: 2.3282 L12: -0.0892 REMARK 3 L13: -0.0225 L23: 0.0276 REMARK 3 S TENSOR REMARK 3 S11: -0.0079 S12: -0.0275 S13: -0.0785 REMARK 3 S21: -0.0086 S22: -0.0446 S23: 0.1686 REMARK 3 S31: -0.1349 S32: -0.0444 S33: 0.0525 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 1 THROUGH 11) REMARK 3 ORIGIN FOR THE GROUP (A): 4.9906 9.7747 -17.3869 REMARK 3 T TENSOR REMARK 3 T11: 0.8459 T22: 0.8298 REMARK 3 T33: 0.7495 T12: -0.0044 REMARK 3 T13: -0.1068 T23: 0.1115 REMARK 3 L TENSOR REMARK 3 L11: 4.0718 L22: 5.1077 REMARK 3 L33: 4.6849 L12: -0.2756 REMARK 3 L13: 0.2191 L23: -0.1855 REMARK 3 S TENSOR REMARK 3 S11: -0.0126 S12: -0.3203 S13: 0.2491 REMARK 3 S21: 0.2023 S22: -0.2232 S23: 1.5871 REMARK 3 S31: -1.1115 S32: -0.8031 S33: 0.2494 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'C' AND RESID 1 THROUGH 12) REMARK 3 ORIGIN FOR THE GROUP (A): 3.8986 11.5806 -16.9954 REMARK 3 T TENSOR REMARK 3 T11: 0.8730 T22: 0.9305 REMARK 3 T33: 0.7491 T12: 0.1343 REMARK 3 T13: -0.1476 T23: 0.0399 REMARK 3 L TENSOR REMARK 3 L11: 3.9565 L22: 4.3518 REMARK 3 L33: 7.0069 L12: -0.4090 REMARK 3 L13: 1.2104 L23: -0.9487 REMARK 3 S TENSOR REMARK 3 S11: 0.2694 S12: -0.1691 S13: -0.2300 REMARK 3 S21: -0.2373 S22: 0.1873 S23: 1.2877 REMARK 3 S31: 0.1534 S32: -0.8591 S33: -0.3909 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 7NE3 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_1292113612. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUN-18 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 : PETRA III, DESY REMARK 200 BEAMLINE : P11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033200 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26450 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.260 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : 0.12900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.26 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 12.70 REMARK 200 R MERGE FOR SHELL (I) : 1.57100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 4NM6 REMARK 200 REMARK 200 REMARK: UNIT CELL: (47.994, 87.711, 260.531, 90, 90, 90) REMARK 200 SPACE GROUP: C 2 2 21 (NO. 20) REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES PH6.3, 23% PEG2000MME, VAPOR REMARK 280 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 130.26550 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 130.26550 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 23.99700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.85550 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 23.99700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.85550 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 130.26550 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 23.99700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 43.85550 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 130.26550 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 23.99700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 43.85550 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: 6080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 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 GLU A 1137 REMARK 465 GLN A 1138 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 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 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 ILE A1139 CG1 CG2 CD1 REMARK 470 LYS A1243 CG CD CE NZ REMARK 470 LYS A1254 CG CD CE NZ REMARK 470 LEU A1258 CG CD1 CD2 REMARK 470 LYS A1304 CG CD CE NZ REMARK 470 ILE A1305 CG1 CG2 CD1 REMARK 470 ASP A1314 CG OD1 OD2 REMARK 470 GLU A1405 CG CD OE1 OE2 REMARK 470 LYS A1409 CG CD CE NZ REMARK 470 ARG A1451 CG CD NE CZ NH1 NH2 REMARK 470 ARG A1452 CG CD NE CZ NH1 NH2 REMARK 470 LYS A1453 CG CD CE NZ REMARK 470 VAL A1461 CG1 CG2 REMARK 470 CYS A1464 SG REMARK 470 ARG A1465 CG CD NE CZ NH1 NH2 REMARK 470 ASP A1849 CG OD1 OD2 REMARK 470 LYS A1887 CG CD CE NZ REMARK 470 LYS A1911 CG CD CE NZ REMARK 470 LYS A1920 CG CD CE NZ REMARK 470 GLU A1923 CG CD OE1 OE2 REMARK 470 LYS A1924 CG CD CE NZ 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 A1141 -167.05 -121.16 REMARK 500 GLU A1234 74.13 -103.01 REMARK 500 ILE A1305 82.59 55.93 REMARK 500 SER A1850 11.84 -149.58 REMARK 500 SER A1850 11.99 -149.58 REMARK 500 ASN A1890 95.30 -160.17 REMARK 500 HIS A1893 65.41 -154.77 REMARK 500 MET A1907 44.12 -105.49 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 A2342 DISTANCE = 6.63 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A2002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1133 SG REMARK 620 2 CYS A1135 SG 107.0 REMARK 620 3 HIS A1219 ND1 88.9 106.5 REMARK 620 4 CYS A1221 SG 111.4 114.8 124.3 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 118.1 REMARK 620 3 CYS A1273 SG 102.6 110.1 REMARK 620 4 HIS A1380 NE2 109.9 99.9 117.1 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 114.0 REMARK 620 3 CYS A1358 SG 111.9 110.7 REMARK 620 4 HIS A1912 ND1 108.5 108.3 102.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 A2004 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A1382 NE2 REMARK 620 2 ASP A1384 OD1 85.1 REMARK 620 3 HIS A1881 NE2 92.0 103.0 REMARK 620 4 OGA A2005 O1 86.7 96.3 160.4 REMARK 620 5 OGA A2005 O2' 96.2 169.1 87.8 73.0 REMARK 620 6 HOH A2203 O 169.6 105.1 88.0 89.9 73.4 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NM6 RELATED DB: PDB REMARK 900 4NM6 CONTAINS THE SAME PROTEIN WITH DIFFERENT DNA OLIGO. DBREF 7NE3 A 1129 1828 UNP Q6N021 TET2_HUMAN 1129 1480 DBREF 7NE3 A 1844 1936 UNP Q6N021 TET2_HUMAN 1844 1936 DBREF 7NE3 B 1 12 PDB 7NE3 7NE3 1 12 DBREF 7NE3 C 1 12 PDB 7NE3 7NE3 1 12 SEQADV 7NE3 GLY A 1126 UNP Q6N021 EXPRESSION TAG SEQADV 7NE3 GLY A 1127 UNP Q6N021 EXPRESSION TAG SEQADV 7NE3 SER A 1128 UNP Q6N021 EXPRESSION TAG SEQADV 7NE3 GLY A 1829 UNP Q6N021 LINKER SEQADV 7NE3 GLY A 1830 UNP Q6N021 LINKER SEQADV 7NE3 GLY A 1831 UNP Q6N021 LINKER SEQADV 7NE3 GLY A 1832 UNP Q6N021 LINKER SEQADV 7NE3 SER A 1833 UNP Q6N021 LINKER SEQADV 7NE3 GLY A 1834 UNP Q6N021 LINKER SEQADV 7NE3 GLY A 1835 UNP Q6N021 LINKER SEQADV 7NE3 GLY A 1836 UNP Q6N021 LINKER SEQADV 7NE3 GLY A 1837 UNP Q6N021 LINKER SEQADV 7NE3 SER A 1838 UNP Q6N021 LINKER SEQADV 7NE3 GLY A 1839 UNP Q6N021 LINKER SEQADV 7NE3 GLY A 1840 UNP Q6N021 LINKER SEQADV 7NE3 GLY A 1841 UNP Q6N021 LINKER SEQADV 7NE3 GLY A 1842 UNP Q6N021 LINKER SEQADV 7NE3 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 DC DA 5CM DG DT DG DT DG DT SEQRES 1 C 12 DA DC DA DC DA 5CM DG DT DG 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 FE2 A2004 1 HET OGA A2005 10 HET EDO A2006 4 HET EDO A2007 4 HET MES A2008 12 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM ZN ZINC ION HETNAM FE2 FE (II) ION HETNAM OGA N-OXALYLGLYCINE HETNAM EDO 1,2-ETHANEDIOL HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 2 5CM 2(C10 H16 N3 O7 P) FORMUL 4 ZN 3(ZN 2+) FORMUL 7 FE2 FE 2+ FORMUL 8 OGA C4 H5 N O5 FORMUL 9 EDO 2(C2 H6 O2) FORMUL 11 MES C6 H13 N O4 S FORMUL 12 HOH *260(H2 O) HELIX 1 AA1 ASN A 1156 GLY A 1169 1 14 HELIX 2 AA2 PRO A 1237 GLY A 1256 1 20 HELIX 3 AA3 ARG A 1261 LEU A 1265 5 5 HELIX 4 AA4 PHE A 1300 SER A 1303 5 4 HELIX 5 AA5 ASP A 1315 ALA A 1341 1 27 HELIX 6 AA6 ALA A 1341 GLU A 1350 1 10 HELIX 7 AA7 ALA A 1355 ARG A 1359 5 5 HELIX 8 AA8 GLU A 1401 ARG A 1404 5 4 HELIX 9 AA9 SER A 1431 GLY A 1442 1 12 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 ALA A 1922 1 10 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 VAL A1395 O LEU A1872 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 CYS A1374 O SER A1898 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 TRP A1198 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 SER A1848 N ARG A1452 LINK O3' DA B 5 P 5CM B 6 1555 1555 1.61 LINK O3' 5CM B 6 P DG B 7 1555 1555 1.61 LINK O3' DA C 5 P 5CM C 6 1555 1555 1.60 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 2.51 LINK SG CYS A1193 ZN ZN A2001 1555 1555 2.37 LINK ND1 HIS A1219 ZN ZN A2002 1555 1555 2.03 LINK SG CYS A1221 ZN ZN A2002 1555 1555 2.15 LINK SG CYS A1271 ZN ZN A2001 1555 1555 2.32 LINK SG CYS A1273 ZN ZN A2001 1555 1555 2.19 LINK SG CYS A1289 ZN ZN A2003 1555 1555 2.42 LINK SG CYS A1298 ZN ZN A2003 1555 1555 2.25 LINK SG CYS A1358 ZN ZN A2003 1555 1555 2.36 LINK NE2 HIS A1380 ZN ZN A2001 1555 1555 2.02 LINK NE2 HIS A1382 FE FE2 A2004 1555 1555 2.31 LINK OD1 ASP A1384 FE FE2 A2004 1555 1555 2.45 LINK NE2 HIS A1881 FE FE2 A2004 1555 1555 2.24 LINK ND1 HIS A1912 ZN ZN A2003 1555 1555 2.10 LINK FE FE2 A2004 O1 OGA A2005 1555 1555 2.33 LINK FE FE2 A2004 O2' OGA A2005 1555 1555 2.27 LINK FE FE2 A2004 O HOH A2203 1555 1555 2.44 CRYST1 47.994 87.711 260.531 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 0.020836 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011401 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003838 0.00000