HEADER OXIDOREDUCTASE/DNA 19-AUG-15 5D9Y TITLE CRYSTAL STRUCTURE OF TET2-5FC COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYLCYTOSINE DIOXYGENASE TET2,METHYLCYTOSINE DIOXYGENASE COMPND 3 TET2; COMPND 4 CHAIN: A; COMPND 5 EC: 1.14.11.-,1.14.11.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*AP*CP*TP*GP*TP*(5FC)P*GP*AP*AP*GP*CP*T)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*AP*GP*CP*TP*TP*CP*GP*AP*CP*AP*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 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630 KEYWDS 5-METHYLCYTOSINE DIOXYGENASE, TET2, 5-FORMYLCYTOSINE, PROTEIN-DNA KEYWDS 2 COMPLEX, 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 5D9Y 1 REMARK REVDAT 2 18-NOV-15 5D9Y 1 JRNL REMARK REVDAT 1 04-NOV-15 5D9Y 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. 1.97 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) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 74.5 REMARK 3 NUMBER OF REFLECTIONS : 57919 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.380 REMARK 3 FREE R VALUE TEST SET COUNT : 3114 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 36.7732 - 5.5156 0.99 3296 195 0.1643 0.2272 REMARK 3 2 5.5156 - 4.3802 0.99 3312 200 0.1535 0.2078 REMARK 3 3 4.3802 - 3.8272 1.00 3321 200 0.1574 0.1959 REMARK 3 4 3.8272 - 3.4775 0.99 3318 188 0.1775 0.2192 REMARK 3 5 3.4775 - 3.2284 1.00 3338 183 0.2057 0.2325 REMARK 3 6 3.2284 - 3.0382 1.00 3336 179 0.2144 0.2420 REMARK 3 7 3.0382 - 2.8861 1.00 3384 185 0.2279 0.2643 REMARK 3 8 2.8861 - 2.7605 0.97 3210 176 0.2336 0.2986 REMARK 3 9 2.7605 - 2.6543 0.96 3179 176 0.2397 0.2834 REMARK 3 10 2.6543 - 2.5627 0.93 3152 167 0.2430 0.3044 REMARK 3 11 2.5627 - 2.4826 0.87 2887 171 0.2340 0.2963 REMARK 3 12 2.4826 - 2.4116 0.81 2678 146 0.2387 0.2460 REMARK 3 13 2.4116 - 2.3482 0.74 2498 139 0.2436 0.3249 REMARK 3 14 2.3482 - 2.2909 0.66 2164 135 0.2534 0.3159 REMARK 3 15 2.2909 - 2.2388 0.60 2060 115 0.2623 0.2982 REMARK 3 16 2.2388 - 2.1912 0.54 1778 100 0.2767 0.3084 REMARK 3 17 2.1912 - 2.1473 0.51 1713 96 0.2898 0.3028 REMARK 3 18 2.1473 - 2.1068 0.45 1493 89 0.2875 0.3349 REMARK 3 19 2.1068 - 2.0692 0.41 1365 81 0.2964 0.3099 REMARK 3 20 2.0692 - 2.0341 0.38 1268 75 0.3000 0.2942 REMARK 3 21 2.0341 - 2.0013 0.33 1050 61 0.2939 0.3174 REMARK 3 22 2.0013 - 1.9705 0.29 1005 57 0.3000 0.3612 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) : 29.400 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.08 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.62 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 : 0.009 3900 REMARK 3 ANGLE : 1.159 5364 REMARK 3 CHIRALITY : 0.045 580 REMARK 3 PLANARITY : 0.005 620 REMARK 3 DIHEDRAL : 19.428 1517 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5D9Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212869. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-14 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 : SSRF REMARK 200 BEAMLINE : BL19U1 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57919 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 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 (%) : 98.9 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.62400 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 (%): 49.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21% PEGMME2000, 0.1M MES, PH 6.3, 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 134.01000 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 134.01000 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 24.07700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.97900 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 24.07700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.97900 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 134.01000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 24.07700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 43.97900 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 134.01000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 24.07700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 43.97900 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: 4350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DC C 9 O3' DC C 9 C3' -0.038 REMARK 500 REMARK 500 REMARK: NULL 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 1 O4' - C1' - N9 ANGL. DEV. = 3.5 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 LYS A1304 -71.49 -49.89 REMARK 500 HIS A1893 65.07 -161.10 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 A2003 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1133 SG REMARK 620 2 CYS A1135 SG 105.9 REMARK 620 3 HIS A1219 ND1 88.6 101.9 REMARK 620 4 CYS A1221 SG 119.7 107.3 130.1 REMARK 620 N 1 2 3 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 A1193 SG REMARK 620 2 CYS A1271 SG 118.8 REMARK 620 3 CYS A1273 SG 104.6 114.7 REMARK 620 4 HIS A1380 NE2 108.9 96.7 113.2 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 A1289 SG REMARK 620 2 CYS A1298 SG 112.9 REMARK 620 3 CYS A1358 SG 115.0 114.6 REMARK 620 4 HIS A1912 ND1 102.9 107.7 102.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A2002 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A1382 NE2 REMARK 620 2 ASP A1384 OD2 106.9 REMARK 620 3 HIS A1881 NE2 96.3 95.1 REMARK 620 4 OGA A2001 O1 85.9 114.4 148.5 REMARK 620 5 OGA A2001 O2' 102.7 150.2 78.1 70.8 REMARK 620 6 HOH A2136 O 177.2 76.0 83.6 92.6 74.5 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 FE A 2002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5DEU RELATED DB: PDB DBREF 5D9Y A 1129 1828 UNP Q6N021 TET2_HUMAN 1129 1480 DBREF 5D9Y A 1844 1936 UNP Q6N021 TET2_HUMAN 1844 1936 DBREF 5D9Y B 1 12 PDB 5D9Y 5D9Y 1 12 DBREF 5D9Y C 1 12 PDB 5D9Y 5D9Y 1 12 SEQADV 5D9Y GLY A 1127 UNP Q6N021 EXPRESSION TAG SEQADV 5D9Y SER A 1128 UNP Q6N021 EXPRESSION TAG SEQADV 5D9Y GLY A 1829 UNP Q6N021 LINKER SEQADV 5D9Y GLY A 1830 UNP Q6N021 LINKER SEQADV 5D9Y GLY A 1831 UNP Q6N021 LINKER SEQADV 5D9Y GLY A 1832 UNP Q6N021 LINKER SEQADV 5D9Y SER A 1833 UNP Q6N021 LINKER SEQADV 5D9Y GLY A 1834 UNP Q6N021 LINKER SEQADV 5D9Y GLY A 1835 UNP Q6N021 LINKER SEQADV 5D9Y GLY A 1836 UNP Q6N021 LINKER SEQADV 5D9Y GLY A 1837 UNP Q6N021 LINKER SEQADV 5D9Y SER A 1838 UNP Q6N021 LINKER SEQADV 5D9Y GLY A 1839 UNP Q6N021 LINKER SEQADV 5D9Y GLY A 1840 UNP Q6N021 LINKER SEQADV 5D9Y GLY A 1841 UNP Q6N021 LINKER SEQADV 5D9Y GLY A 1842 UNP Q6N021 LINKER SEQADV 5D9Y SER A 1843 UNP Q6N021 LINKER 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 DT DG DT 5FC DG DA DA DG DC DT SEQRES 1 C 12 DA DG DC DT DT DC DG DA DC DA DG DT HET 5FC B 6 21 HET OGA A2001 10 HET FE A2002 1 HET ZN A2003 1 HET ZN A2004 1 HET ZN A2005 1 HETNAM 5FC 5-FORMYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM OGA N-OXALYLGLYCINE HETNAM FE FE (III) ION HETNAM ZN ZINC ION HETSYN 5FC 2'-DEOXY-5-FORMYLCYTIDINE-5'-MONOPHOSPHATE FORMUL 2 5FC C10 H14 N3 O8 P FORMUL 4 OGA C4 H5 N O5 FORMUL 5 FE FE 3+ FORMUL 6 ZN 3(ZN 2+) FORMUL 9 HOH *262(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 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 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 1919 1 7 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 SER A1848 N ARG A1452 LINK O3' DT B 5 P 5FC B 6 1555 1555 1.61 LINK O3' 5FC B 6 P DG B 7 1555 1555 1.62 LINK SG CYS A1133 ZN ZN A2003 1555 1555 2.24 LINK SG CYS A1135 ZN ZN A2003 1555 1555 2.58 LINK SG CYS A1193 ZN ZN A2004 1555 1555 2.37 LINK ND1 HIS A1219 ZN ZN A2003 1555 1555 2.10 LINK SG CYS A1221 ZN ZN A2003 1555 1555 2.11 LINK SG CYS A1271 ZN ZN A2004 1555 1555 2.19 LINK SG CYS A1273 ZN ZN A2004 1555 1555 2.17 LINK SG CYS A1289 ZN ZN A2005 1555 1555 2.32 LINK SG CYS A1298 ZN ZN A2005 1555 1555 2.21 LINK SG CYS A1358 ZN ZN A2005 1555 1555 2.41 LINK NE2 HIS A1380 ZN ZN A2004 1555 1555 2.11 LINK NE2 HIS A1382 FE FE A2002 1555 1555 2.27 LINK OD2 ASP A1384 FE FE A2002 1555 1555 2.12 LINK NE2 HIS A1881 FE FE A2002 1555 1555 2.17 LINK ND1 HIS A1912 ZN ZN A2005 1555 1555 2.15 LINK O1 OGA A2001 FE FE A2002 1555 1555 2.36 LINK O2' OGA A2001 FE FE A2002 1555 1555 2.17 LINK FE FE A2002 O HOH A2136 1555 1555 2.06 CISPEP 1 SER A 1132 CYS A 1133 0 7.96 SITE 1 AC1 13 ARG A1261 CYS A1374 HIS A1382 ASP A1384 SITE 2 AC1 13 HIS A1416 HIS A1881 THR A1883 ARG A1896 SITE 3 AC1 13 SER A1898 FE A2002 HOH A2136 HOH A2255 SITE 4 AC1 13 5FC B 6 SITE 1 AC2 5 HIS A1382 ASP A1384 HIS A1881 OGA A2001 SITE 2 AC2 5 HOH A2136 SITE 1 AC3 4 CYS A1133 CYS A1135 HIS A1219 CYS A1221 SITE 1 AC4 4 CYS A1193 CYS A1271 CYS A1273 HIS A1380 SITE 1 AC5 4 CYS A1289 CYS A1298 CYS A1358 HIS A1912 CRYST1 48.154 87.958 268.020 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 0.020767 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011369 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003731 0.00000