HEADER TRANSCRIPTION REGULATOR/DNA 11-DEC-14 4X9J TITLE EGR-1 WITH DOUBLY METHYLATED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: EARLY GROWTH RESPONSE PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 335-423; COMPND 5 SYNONYM: EGR-1,AT225,NERVE GROWTH FACTOR-INDUCED PROTEIN A,NGFI-A, COMPND 6 TRANSCRIPTION FACTOR ETR103,TRANSCRIPTION FACTOR ZIF268,ZINC FINGER COMPND 7 PROTEIN 225,ZINC FINGER PROTEIN KROX-24; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(*AP*GP*(5CM)P*GP*TP*GP*GP*GP*(5CM)P*GP*T)-3'); COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*TP*AP*(5CM)P*GP*CP*CP*CP*AP*(5CM)P*GP*C)-3'); COMPND 15 CHAIN: C; COMPND 16 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: EGR1, KROX24, ZNF225; 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 DNA BINDING, METHYLATED DNA, ZINC FINGER, TRANSCRIPTION, KEYWDS 2 TRANSCRIPTION REGULATOR-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.A.WHITE,L.ZANDARASHVILI,J.IWAHARA REVDAT 5 27-SEP-23 4X9J 1 DBREF REVDAT 4 27-SEP-17 4X9J 1 SOURCE JRNL REMARK REVDAT 3 15-JUL-15 4X9J 1 JRNL REVDAT 2 03-JUN-15 4X9J 1 JRNL REVDAT 1 13-MAY-15 4X9J 0 JRNL AUTH L.ZANDARASHVILI,M.A.WHITE,A.ESADZE,J.IWAHARA JRNL TITL STRUCTURAL IMPACT OF COMPLETE CPG METHYLATION WITHIN TARGET JRNL TITL 2 DNA ON SPECIFIC COMPLEX FORMATION OF THE INDUCIBLE JRNL TITL 3 TRANSCRIPTION FACTOR EGR-1. JRNL REF FEBS LETT. V. 589 1748 2015 JRNL REFN ISSN 0014-5793 JRNL PMID 25999311 JRNL DOI 10.1016/J.FEBSLET.2015.05.022 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.HASHIMOTO,Y.O.OLANREWAJU,Y.ZHENG,G.G.WILSON,X.ZHANG, REMARK 1 AUTH 2 X.CHENG REMARK 1 TITL WILMS TUMOR PROTEIN RECOGNIZES 5-CARBOXYLCYTOSINE WITHIN A REMARK 1 TITL 2 SPECIFIC DNA SEQUENCE. REMARK 1 REF GENES DEV. V. 28 2304 2014 REMARK 1 REFN ISSN 1549-5477 REMARK 1 PMID 25258363 REMARK 1 DOI 10.1101/GAD.250746.114 REMARK 2 REMARK 2 RESOLUTION. 1.41 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1810) 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) : 1.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 78.8 REMARK 3 NUMBER OF REFLECTIONS : 46626 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.480 REMARK 3 FREE R VALUE TEST SET COUNT : 3489 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 27.3624 - 4.1238 0.97 2126 177 0.1453 0.1643 REMARK 3 2 4.1238 - 3.2749 0.99 2145 171 0.1467 0.1785 REMARK 3 3 3.2749 - 2.8615 1.00 2213 181 0.1756 0.2207 REMARK 3 4 2.8615 - 2.6001 1.00 2183 176 0.1842 0.2199 REMARK 3 5 2.6001 - 2.4138 1.00 2183 175 0.1775 0.2143 REMARK 3 6 2.4138 - 2.2716 1.00 2181 177 0.1626 0.1760 REMARK 3 7 2.2716 - 2.1579 1.00 2200 178 0.1646 0.1861 REMARK 3 8 2.1579 - 2.0640 1.00 2175 179 0.1755 0.2006 REMARK 3 9 2.0640 - 1.9845 1.00 2180 177 0.1752 0.1908 REMARK 3 10 1.9845 - 1.9161 1.00 2206 179 0.1905 0.2108 REMARK 3 11 1.9161 - 1.8562 1.00 2173 182 0.1824 0.2033 REMARK 3 12 1.8562 - 1.8031 1.00 2172 175 0.1766 0.2310 REMARK 3 13 1.8031 - 1.7557 1.00 2191 176 0.1801 0.1998 REMARK 3 14 1.7557 - 1.7128 0.98 2145 171 0.1749 0.2672 REMARK 3 15 1.7128 - 1.6739 0.96 2098 172 0.1871 0.1808 REMARK 3 16 1.6739 - 1.6383 0.96 2094 169 0.1847 0.2228 REMARK 3 17 1.6383 - 1.6055 0.90 1979 163 0.1921 0.2020 REMARK 3 18 1.6055 - 1.5752 0.79 1750 132 0.1904 0.2235 REMARK 3 19 1.5752 - 1.5471 0.67 1457 118 0.1966 0.2346 REMARK 3 20 1.5471 - 1.5209 0.50 1091 84 0.2256 0.2560 REMARK 3 21 1.5209 - 1.4963 0.37 816 66 0.2350 0.2356 REMARK 3 22 1.4963 - 1.4733 0.30 663 54 0.2466 0.2765 REMARK 3 23 1.4733 - 1.4517 0.21 464 37 0.2539 0.2572 REMARK 3 24 1.4517 - 1.4312 0.10 219 17 0.2704 0.3119 REMARK 3 25 1.4312 - 1.4119 0.01 33 3 0.3055 0.3441 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.460 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.013 1283 REMARK 3 ANGLE : 1.338 1827 REMARK 3 CHIRALITY : 0.071 190 REMARK 3 PLANARITY : 0.032 163 REMARK 3 DIHEDRAL : 22.003 505 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 10 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 102:125) REMARK 3 ORIGIN FOR THE GROUP (A): 6.4181 -6.2665 -3.4961 REMARK 3 T TENSOR REMARK 3 T11: 0.2102 T22: 0.1615 REMARK 3 T33: 0.0661 T12: -0.0224 REMARK 3 T13: -0.0399 T23: -0.0193 REMARK 3 L TENSOR REMARK 3 L11: 0.0059 L22: 0.0089 REMARK 3 L33: 0.0101 L12: -0.0068 REMARK 3 L13: 0.0063 L23: -0.0086 REMARK 3 S TENSOR REMARK 3 S11: -0.0244 S12: -0.0201 S13: 0.0094 REMARK 3 S21: 0.0315 S22: 0.0029 S23: -0.0002 REMARK 3 S31: 0.0382 S32: 0.0191 S33: -0.0107 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 126:133) REMARK 3 ORIGIN FOR THE GROUP (A): -5.5280 -2.5466 -5.0991 REMARK 3 T TENSOR REMARK 3 T11: 0.2525 T22: 0.2810 REMARK 3 T33: 0.1470 T12: -0.0512 REMARK 3 T13: -0.0103 T23: -0.0827 REMARK 3 L TENSOR REMARK 3 L11: 0.0011 L22: 0.0007 REMARK 3 L33: 0.0018 L12: -0.0003 REMARK 3 L13: 0.0013 L23: 0.0000 REMARK 3 S TENSOR REMARK 3 S11: -0.0025 S12: -0.0024 S13: 0.0014 REMARK 3 S21: -0.0037 S22: -0.0129 S23: 0.0056 REMARK 3 S31: -0.0044 S32: -0.0047 S33: -0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 134:143) REMARK 3 ORIGIN FOR THE GROUP (A): -15.7982 -1.6767 -17.0065 REMARK 3 T TENSOR REMARK 3 T11: 0.1381 T22: 0.1949 REMARK 3 T33: 0.1460 T12: -0.0398 REMARK 3 T13: -0.0064 T23: -0.0740 REMARK 3 L TENSOR REMARK 3 L11: 0.0003 L22: 0.0011 REMARK 3 L33: 0.0005 L12: -0.0005 REMARK 3 L13: -0.0001 L23: 0.0002 REMARK 3 S TENSOR REMARK 3 S11: -0.0098 S12: 0.0066 S13: 0.0108 REMARK 3 S21: 0.0104 S22: -0.0106 S23: -0.0052 REMARK 3 S31: -0.0156 S32: -0.0056 S33: 0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 144:166) REMARK 3 ORIGIN FOR THE GROUP (A): -9.8020 -10.5535 -24.3116 REMARK 3 T TENSOR REMARK 3 T11: 0.0907 T22: 0.1131 REMARK 3 T33: 0.0845 T12: -0.0293 REMARK 3 T13: 0.0013 T23: -0.0048 REMARK 3 L TENSOR REMARK 3 L11: 0.0018 L22: 0.0089 REMARK 3 L33: 0.0029 L12: -0.0001 REMARK 3 L13: -0.0012 L23: -0.0022 REMARK 3 S TENSOR REMARK 3 S11: 0.0134 S12: -0.0205 S13: 0.0415 REMARK 3 S21: -0.0069 S22: -0.0562 S23: -0.0088 REMARK 3 S31: -0.0440 S32: 0.0681 S33: -0.0097 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 167:178) REMARK 3 ORIGIN FOR THE GROUP (A): -7.3987 -20.7040 -29.4115 REMARK 3 T TENSOR REMARK 3 T11: 0.0635 T22: 0.1171 REMARK 3 T33: 0.0730 T12: -0.0113 REMARK 3 T13: -0.0000 T23: -0.0006 REMARK 3 L TENSOR REMARK 3 L11: 0.0004 L22: 0.0009 REMARK 3 L33: 0.0008 L12: -0.0003 REMARK 3 L13: -0.0000 L23: -0.0001 REMARK 3 S TENSOR REMARK 3 S11: -0.0091 S12: 0.0117 S13: -0.0049 REMARK 3 S21: 0.0114 S22: -0.0188 S23: -0.0110 REMARK 3 S31: -0.0152 S32: 0.0097 S33: -0.0019 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 179:187) REMARK 3 ORIGIN FOR THE GROUP (A): -3.5278 -30.2563 -27.6462 REMARK 3 T TENSOR REMARK 3 T11: 0.0556 T22: 0.0904 REMARK 3 T33: 0.0800 T12: 0.0035 REMARK 3 T13: 0.0332 T23: 0.0110 REMARK 3 L TENSOR REMARK 3 L11: 0.0095 L22: 0.0112 REMARK 3 L33: 0.0062 L12: -0.0020 REMARK 3 L13: -0.0069 L23: -0.0002 REMARK 3 S TENSOR REMARK 3 S11: -0.0033 S12: -0.0084 S13: -0.0105 REMARK 3 S21: 0.0046 S22: -0.0137 S23: -0.0073 REMARK 3 S31: 0.0111 S32: 0.0106 S33: 0.0012 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN B AND RESID 1:5) REMARK 3 ORIGIN FOR THE GROUP (A): -12.0992 -17.7784 -17.8239 REMARK 3 T TENSOR REMARK 3 T11: 0.1367 T22: 0.1164 REMARK 3 T33: 0.0960 T12: -0.1482 REMARK 3 T13: -0.0015 T23: 0.0047 REMARK 3 L TENSOR REMARK 3 L11: 0.0130 L22: 0.0016 REMARK 3 L33: 0.0018 L12: 0.0035 REMARK 3 L13: -0.0008 L23: -0.0014 REMARK 3 S TENSOR REMARK 3 S11: -0.0014 S12: -0.0100 S13: -0.0115 REMARK 3 S21: -0.0035 S22: -0.0056 S23: 0.0196 REMARK 3 S31: 0.0037 S32: 0.0003 S33: -0.0110 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN B AND RESID 6:11) REMARK 3 ORIGIN FOR THE GROUP (A): 5.8325 -9.5535 -16.1096 REMARK 3 T TENSOR REMARK 3 T11: 0.1461 T22: 0.1111 REMARK 3 T33: 0.1365 T12: -0.1292 REMARK 3 T13: 0.0199 T23: 0.0372 REMARK 3 L TENSOR REMARK 3 L11: 0.0002 L22: 0.0011 REMARK 3 L33: 0.0060 L12: 0.0000 REMARK 3 L13: 0.0019 L23: -0.0018 REMARK 3 S TENSOR REMARK 3 S11: 0.0079 S12: -0.0278 S13: -0.0256 REMARK 3 S21: -0.0108 S22: -0.0013 S23: -0.0227 REMARK 3 S31: 0.0149 S32: -0.0111 S33: 0.0254 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN C AND RESID 51:56) REMARK 3 ORIGIN FOR THE GROUP (A): 1.9398 -5.6107 -21.0824 REMARK 3 T TENSOR REMARK 3 T11: 0.1443 T22: 0.1010 REMARK 3 T33: 0.1127 T12: -0.1285 REMARK 3 T13: 0.0084 T23: -0.0215 REMARK 3 L TENSOR REMARK 3 L11: 0.0034 L22: 0.0083 REMARK 3 L33: 0.0075 L12: 0.0036 REMARK 3 L13: 0.0011 L23: -0.0036 REMARK 3 S TENSOR REMARK 3 S11: -0.0112 S12: -0.0029 S13: 0.0118 REMARK 3 S21: -0.0030 S22: -0.0139 S23: 0.0020 REMARK 3 S31: -0.0086 S32: 0.0056 S33: -0.0337 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN C AND RESID 57:61) REMARK 3 ORIGIN FOR THE GROUP (A): -3.4961 -20.8602 -13.7105 REMARK 3 T TENSOR REMARK 3 T11: 0.1344 T22: 0.1201 REMARK 3 T33: 0.0946 T12: -0.1056 REMARK 3 T13: -0.0128 T23: 0.0360 REMARK 3 L TENSOR REMARK 3 L11: 0.0167 L22: 0.0121 REMARK 3 L33: 0.0004 L12: 0.0107 REMARK 3 L13: 0.0004 L23: -0.0004 REMARK 3 S TENSOR REMARK 3 S11: 0.0020 S12: -0.0158 S13: -0.0018 REMARK 3 S21: 0.0055 S22: -0.0056 S23: -0.0160 REMARK 3 S31: 0.0039 S32: 0.0001 S33: -0.0048 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 4X9J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1000204827. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 7-8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : SI DCM REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29071 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 43.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.6 REMARK 200 DATA REDUNDANCY : 15.40 REMARK 200 R MERGE (I) : 0.12700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 46.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.65300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 4R2A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25MM BISTRIS PH8, 10% PEG-600, 450MM REMARK 280 NACL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K 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 64.47600 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 64.47600 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 22.00450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.99450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 22.00450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.99450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 64.47600 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 22.00450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 27.99450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 64.47600 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 22.00450 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 27.99450 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 642 LIES ON A SPECIAL POSITION. 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 GLN A 188 REMARK 465 LYS A 189 REMARK 465 ASP A 190 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OP2 5CM B 3 O HOH B 132 1.99 REMARK 500 NH1 ARG A 178 O HOH A 601 2.13 REMARK 500 OP2 DC C 57 O HOH C 101 2.13 REMARK 500 OP2 DA C 58 O HOH C 146 2.15 REMARK 500 OE2 GLU A 177 O HOH A 691 2.16 REMARK 500 O HOH C 129 O HOH C 139 2.18 REMARK 500 OP1 DC C 56 O HOH C 102 2.18 REMARK 500 OP2 DG B 7 O HOH B 143 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 DG C 54 O3' DG C 54 C3' -0.062 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 DT B 5 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT B 11 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG C 54 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES 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 A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 107 SG REMARK 620 2 CYS A 112 SG 112.7 REMARK 620 3 HIS A 125 NE2 109.0 109.9 REMARK 620 4 HIS A 129 NE2 105.2 121.4 97.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 137 SG REMARK 620 2 CYS A 140 SG 114.9 REMARK 620 3 HIS A 153 NE2 108.7 108.4 REMARK 620 4 HIS A 157 NE2 111.5 111.1 101.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 165 SG REMARK 620 2 CYS A 168 SG 113.4 REMARK 620 3 HIS A 181 NE2 106.5 107.0 REMARK 620 4 HIS A 185 NE2 108.2 115.2 105.9 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4R2A RELATED DB: PDB REMARK 900 SAME PROTEIN WITH SINGLY METHYLATED DNA DBREF 4X9J A 102 190 UNP P18146 EGR1_HUMAN 335 423 DBREF 4X9J B 1 11 PDB 4X9J 4X9J 1 11 DBREF 4X9J C 51 61 PDB 4X9J 4X9J 51 61 SEQRES 1 A 89 GLU ARG PRO TYR ALA CYS PRO VAL GLU SER CYS ASP ARG SEQRES 2 A 89 ARG PHE SER ARG SER ASP GLU LEU THR ARG HIS ILE ARG SEQRES 3 A 89 ILE HIS THR GLY GLN LYS PRO PHE GLN CYS ARG ILE CYS SEQRES 4 A 89 MET ARG ASN PHE SER ARG SER ASP HIS LEU THR THR HIS SEQRES 5 A 89 ILE ARG THR HIS THR GLY GLU LYS PRO PHE ALA CYS ASP SEQRES 6 A 89 ILE CYS GLY ARG LYS PHE ALA ARG SER ASP GLU ARG LYS SEQRES 7 A 89 ARG HIS THR LYS ILE HIS LEU ARG GLN LYS ASP SEQRES 1 B 11 DA DG 5CM DG DT DG DG DG 5CM DG DT SEQRES 1 C 11 DT DA 5CM DG DC DC DC DA 5CM DG DC HET 5CM B 3 33 HET 5CM B 9 33 HET 5CM C 53 33 HET 5CM C 59 33 HET ZN A 501 1 HET ZN A 502 1 HET ZN A 503 1 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM ZN ZINC ION FORMUL 2 5CM 4(C10 H16 N3 O7 P) FORMUL 4 ZN 3(ZN 2+) FORMUL 7 HOH *208(H2 O) HELIX 1 AA1 ARG A 118 GLY A 131 1 14 HELIX 2 AA2 ARG A 146 GLY A 159 1 14 HELIX 3 AA3 ARG A 174 LYS A 183 1 10 HELIX 4 AA4 ILE A 184 LEU A 186 5 3 SHEET 1 AA1 2 TYR A 105 ALA A 106 0 SHEET 2 AA1 2 ARG A 115 PHE A 116 -1 O PHE A 116 N TYR A 105 SHEET 1 AA2 2 PHE A 135 GLN A 136 0 SHEET 2 AA2 2 ASN A 143 PHE A 144 -1 O PHE A 144 N PHE A 135 SHEET 1 AA3 2 PHE A 163 ALA A 164 0 SHEET 2 AA3 2 LYS A 171 PHE A 172 -1 O PHE A 172 N PHE A 163 LINK O3' DG B 2 P 5CM B 3 1555 1555 1.60 LINK O3' 5CM B 3 P DG B 4 1555 1555 1.59 LINK O3' DG B 8 P 5CM B 9 1555 1555 1.60 LINK O3' 5CM B 9 P DG B 10 1555 1555 1.59 LINK O3' DA C 52 P 5CM C 53 1555 1555 1.61 LINK O3' 5CM C 53 P DG C 54 1555 1555 1.58 LINK O3' DA C 58 P 5CM C 59 1555 1555 1.60 LINK O3' 5CM C 59 P DG C 60 1555 1555 1.60 LINK SG CYS A 107 ZN ZN A 501 1555 1555 2.28 LINK SG CYS A 112 ZN ZN A 501 1555 1555 2.30 LINK NE2 HIS A 125 ZN ZN A 501 1555 1555 2.03 LINK NE2 HIS A 129 ZN ZN A 501 1555 1555 1.91 LINK SG CYS A 137 ZN ZN A 502 1555 1555 2.34 LINK SG CYS A 140 ZN ZN A 502 1555 1555 2.29 LINK NE2 HIS A 153 ZN ZN A 502 1555 1555 2.07 LINK NE2 HIS A 157 ZN ZN A 502 1555 1555 2.04 LINK SG CYS A 165 ZN ZN A 503 1555 1555 2.35 LINK SG CYS A 168 ZN ZN A 503 1555 1555 2.29 LINK NE2 HIS A 181 ZN ZN A 503 1555 1555 2.03 LINK NE2 HIS A 185 ZN ZN A 503 1555 1555 2.01 SITE 1 AC1 4 CYS A 107 CYS A 112 HIS A 125 HIS A 129 SITE 1 AC2 4 CYS A 137 CYS A 140 HIS A 153 HIS A 157 SITE 1 AC3 4 CYS A 165 CYS A 168 HIS A 181 HIS A 185 CRYST1 44.009 55.989 128.952 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 0.022723 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017861 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007755 0.00000 CONECT 89 2197 CONECT 155 2197 CONECT 379 2197 CONECT 458 2197 CONECT 582 2198 CONECT 635 2198 CONECT 846 2198 CONECT 920 2198 CONECT 1035 2199 CONECT 1076 2199 CONECT 1305 2199 CONECT 1377 2199 CONECT 1467 1509 CONECT 1492 1493 1498 1501 CONECT 1493 1492 1494 1499 CONECT 1494 1493 1495 CONECT 1495 1494 1496 1500 CONECT 1496 1495 1497 1498 CONECT 1497 1496 1512 1513 1514 CONECT 1498 1492 1496 1515 CONECT 1499 1493 CONECT 1500 1495 1516 1517 CONECT 1501 1492 1502 1505 1518 CONECT 1502 1501 1503 1519 1520 CONECT 1503 1502 1504 1506 1521 CONECT 1504 1503 1505 1507 1522 CONECT 1505 1501 1504 CONECT 1506 1503 1525 CONECT 1507 1504 1508 1523 1524 CONECT 1508 1507 1509 CONECT 1509 1467 1508 1510 1511 CONECT 1510 1509 CONECT 1511 1509 CONECT 1512 1497 CONECT 1513 1497 CONECT 1514 1497 CONECT 1515 1498 CONECT 1516 1500 CONECT 1517 1500 CONECT 1518 1501 CONECT 1519 1502 CONECT 1520 1502 CONECT 1521 1503 CONECT 1522 1504 CONECT 1523 1507 CONECT 1524 1507 CONECT 1525 1506 CONECT 1664 1706 CONECT 1689 1690 1695 1698 CONECT 1690 1689 1691 1696 CONECT 1691 1690 1692 CONECT 1692 1691 1693 1697 CONECT 1693 1692 1694 1695 CONECT 1694 1693 1709 1710 1711 CONECT 1695 1689 1693 1712 CONECT 1696 1690 CONECT 1697 1692 1713 1714 CONECT 1698 1689 1699 1702 1715 CONECT 1699 1698 1700 1716 1717 CONECT 1700 1699 1701 1703 1718 CONECT 1701 1700 1702 1704 1719 CONECT 1702 1698 1701 CONECT 1703 1700 1722 CONECT 1704 1701 1705 1720 1721 CONECT 1705 1704 1706 CONECT 1706 1664 1705 1707 1708 CONECT 1707 1706 CONECT 1708 1706 CONECT 1709 1694 CONECT 1710 1694 CONECT 1711 1694 CONECT 1712 1695 CONECT 1713 1697 CONECT 1714 1697 CONECT 1715 1698 CONECT 1716 1699 CONECT 1717 1699 CONECT 1718 1700 CONECT 1719 1701 CONECT 1720 1704 CONECT 1721 1704 CONECT 1722 1703 CONECT 1827 1868 CONECT 1851 1852 1857 1860 CONECT 1852 1851 1853 1858 CONECT 1853 1852 1854 CONECT 1854 1853 1855 1859 CONECT 1855 1854 1856 1857 CONECT 1856 1855 1871 1872 1873 CONECT 1857 1851 1855 1874 CONECT 1858 1852 CONECT 1859 1854 1875 1876 CONECT 1860 1851 1861 1864 1877 CONECT 1861 1860 1862 1878 1879 CONECT 1862 1861 1863 1865 1880 CONECT 1863 1862 1864 1866 1881 CONECT 1864 1860 1863 CONECT 1865 1862 1884 CONECT 1866 1863 1867 1882 1883 CONECT 1867 1866 1868 CONECT 1868 1827 1867 1869 1870 CONECT 1869 1868 CONECT 1870 1868 CONECT 1871 1856 CONECT 1872 1856 CONECT 1873 1856 CONECT 1874 1857 CONECT 1875 1859 CONECT 1876 1859 CONECT 1877 1860 CONECT 1878 1861 CONECT 1879 1861 CONECT 1880 1862 CONECT 1881 1863 CONECT 1882 1866 CONECT 1883 1866 CONECT 1884 1865 CONECT 2075 2116 CONECT 2099 2100 2105 2108 CONECT 2100 2099 2101 2106 CONECT 2101 2100 2102 CONECT 2102 2101 2103 2107 CONECT 2103 2102 2104 2105 CONECT 2104 2103 2119 2120 2121 CONECT 2105 2099 2103 2122 CONECT 2106 2100 CONECT 2107 2102 2123 2124 CONECT 2108 2099 2109 2112 2125 CONECT 2109 2108 2110 2126 2127 CONECT 2110 2109 2111 2113 2128 CONECT 2111 2110 2112 2114 2129 CONECT 2112 2108 2111 CONECT 2113 2110 2132 CONECT 2114 2111 2115 2130 2131 CONECT 2115 2114 2116 CONECT 2116 2075 2115 2117 2118 CONECT 2117 2116 CONECT 2118 2116 CONECT 2119 2104 CONECT 2120 2104 CONECT 2121 2104 CONECT 2122 2105 CONECT 2123 2107 CONECT 2124 2107 CONECT 2125 2108 CONECT 2126 2109 CONECT 2127 2109 CONECT 2128 2110 CONECT 2129 2111 CONECT 2130 2114 CONECT 2131 2114 CONECT 2132 2113 CONECT 2197 89 155 379 458 CONECT 2198 582 635 846 920 CONECT 2199 1035 1076 1305 1377 MASTER 510 0 7 4 6 0 3 6 1381 3 155 9 END