HEADER HYDROLASE/DNA 10-DEC-20 7KZG TITLE HUMAN MBD4 GLYCOSYLASE DOMAIN BOUND TO DNA CONTAINING OXACARBENIUM-ION TITLE 2 ANALOG 1-AZA-2'-DEOXYRIBOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYL-CPG-BINDING DOMAIN PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GLYCOSYLASE DOMAIN (UNP RESIDUES 426-580); COMPND 5 SYNONYM: METHYL-CPG-BINDING ENDONUCLEASE 1,METHYL-CPG-BINDING PROTEIN COMPND 6 MBD4,MISMATCH-SPECIFIC DNA N-GLYCOSYLASE; COMPND 7 EC: 3.2.2.-; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(*CP*CP*AP*GP*CP*GP*(NR1)P*GP*CP*AP*GP*C)-3'); COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*GP*CP*TP*GP*CP*GP*CP*GP*CP*TP*GP*G)-3'); COMPND 15 CHAIN: D; 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: MBD4, MED1; 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: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 16 ORGANISM_COMMON: HUMAN; SOURCE 17 ORGANISM_TAXID: 9606 KEYWDS PROTEIN-DNA COMPLEX, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.S.PIDUGU,E.POZHARSKI,A.C.DROHAT REVDAT 2 18-OCT-23 7KZG 1 REMARK REVDAT 1 10-NOV-21 7KZG 0 JRNL AUTH L.S.PIDUGU,H.BRIGHT,W.J.LIN,C.MAJUMDAR,R.P.VAN OSTRAND, JRNL AUTH 2 S.S.DAVID,E.POZHARSKI,A.C.DROHAT JRNL TITL STRUCTURAL INSIGHTS INTO THE MECHANISM OF BASE EXCISION BY JRNL TITL 2 MBD4. JRNL REF J.MOL.BIOL. V. 433 67097 2021 JRNL REFN ESSN 1089-8638 JRNL PMID 34107280 JRNL DOI 10.1016/J.JMB.2021.167097 REMARK 2 REMARK 2 RESOLUTION. 1.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 1.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 28046 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1429 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 37.9800 - 3.6200 0.99 2852 146 0.1508 0.1871 REMARK 3 2 3.6200 - 2.8700 0.99 2682 146 0.1526 0.1970 REMARK 3 3 2.8700 - 2.5100 1.00 2690 140 0.1587 0.2058 REMARK 3 4 2.5100 - 2.2800 0.99 2635 151 0.1616 0.1906 REMARK 3 5 2.2800 - 2.1200 1.00 2650 154 0.1720 0.2007 REMARK 3 6 2.1200 - 1.9900 1.00 2659 125 0.1739 0.2179 REMARK 3 7 1.9900 - 1.8900 1.00 2621 146 0.1917 0.2260 REMARK 3 8 1.8900 - 1.8100 0.98 2596 132 0.2161 0.2229 REMARK 3 9 1.8100 - 1.7400 1.00 2632 146 0.2354 0.2728 REMARK 3 10 1.7400 - 1.6800 0.99 2600 143 0.2613 0.2662 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.48 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 14 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 437 THROUGH 455 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.2152 17.8493 17.2520 REMARK 3 T TENSOR REMARK 3 T11: 0.1740 T22: 0.1887 REMARK 3 T33: 0.2067 T12: 0.0092 REMARK 3 T13: 0.0014 T23: -0.0048 REMARK 3 L TENSOR REMARK 3 L11: 2.8541 L22: 1.7901 REMARK 3 L33: 2.4986 L12: -0.3262 REMARK 3 L13: 1.1918 L23: 1.0428 REMARK 3 S TENSOR REMARK 3 S11: 0.0405 S12: -0.3053 S13: 0.4972 REMARK 3 S21: 0.0811 S22: -0.0588 S23: 0.0725 REMARK 3 S31: -0.2435 S32: -0.1931 S33: -0.0090 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 456 THROUGH 470 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.5999 6.3229 17.8962 REMARK 3 T TENSOR REMARK 3 T11: 0.0891 T22: 0.1224 REMARK 3 T33: 0.0858 T12: 0.0134 REMARK 3 T13: -0.0076 T23: 0.0073 REMARK 3 L TENSOR REMARK 3 L11: 2.6252 L22: 5.3048 REMARK 3 L33: 2.8507 L12: 1.2101 REMARK 3 L13: 0.0878 L23: 0.2265 REMARK 3 S TENSOR REMARK 3 S11: -0.0495 S12: -0.1089 S13: -0.0707 REMARK 3 S21: -0.0713 S22: 0.0566 S23: 0.0913 REMARK 3 S31: -0.0359 S32: -0.0554 S33: -0.0097 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 471 THROUGH 484 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.6385 6.3150 27.6359 REMARK 3 T TENSOR REMARK 3 T11: 0.1974 T22: 0.1380 REMARK 3 T33: 0.1248 T12: 0.0363 REMARK 3 T13: 0.0423 T23: -0.0031 REMARK 3 L TENSOR REMARK 3 L11: 1.9625 L22: 4.6381 REMARK 3 L33: 5.9029 L12: 2.7472 REMARK 3 L13: 1.7774 L23: 0.9449 REMARK 3 S TENSOR REMARK 3 S11: 0.2776 S12: -0.3949 S13: 0.2455 REMARK 3 S21: 0.5196 S22: -0.1977 S23: 0.2983 REMARK 3 S31: 0.0392 S32: -0.1175 S33: -0.0487 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 485 THROUGH 495 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.0575 9.6175 24.2087 REMARK 3 T TENSOR REMARK 3 T11: 0.1675 T22: 0.1465 REMARK 3 T33: 0.1384 T12: -0.0081 REMARK 3 T13: -0.0427 T23: -0.0344 REMARK 3 L TENSOR REMARK 3 L11: 4.1394 L22: 4.2376 REMARK 3 L33: 4.0078 L12: 0.0939 REMARK 3 L13: -0.1297 L23: 0.3020 REMARK 3 S TENSOR REMARK 3 S11: 0.0480 S12: -0.2630 S13: 0.0939 REMARK 3 S21: 0.4924 S22: -0.0139 S23: -0.3454 REMARK 3 S31: -0.1282 S32: 0.1189 S33: -0.0461 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 496 THROUGH 508 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.5953 -2.7904 25.9434 REMARK 3 T TENSOR REMARK 3 T11: 0.2219 T22: 0.1754 REMARK 3 T33: 0.1393 T12: 0.0524 REMARK 3 T13: -0.0272 T23: 0.0227 REMARK 3 L TENSOR REMARK 3 L11: 2.9258 L22: 4.6707 REMARK 3 L33: 6.7458 L12: 3.4221 REMARK 3 L13: 0.0977 L23: 1.4244 REMARK 3 S TENSOR REMARK 3 S11: 0.0116 S12: -0.5645 S13: -0.1898 REMARK 3 S21: 0.3461 S22: 0.0183 S23: -0.2502 REMARK 3 S31: -0.0470 S32: 0.2441 S33: 0.0004 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 509 THROUGH 525 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.1258 4.0818 17.0816 REMARK 3 T TENSOR REMARK 3 T11: 0.0946 T22: 0.1252 REMARK 3 T33: 0.1125 T12: 0.0173 REMARK 3 T13: -0.0091 T23: -0.0066 REMARK 3 L TENSOR REMARK 3 L11: 2.9918 L22: 6.6237 REMARK 3 L33: 3.5648 L12: 2.7884 REMARK 3 L13: -1.4205 L23: -2.6464 REMARK 3 S TENSOR REMARK 3 S11: -0.0491 S12: -0.0022 S13: -0.0596 REMARK 3 S21: -0.1549 S22: -0.0025 S23: -0.3047 REMARK 3 S31: 0.1108 S32: 0.2386 S33: 0.0649 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 526 THROUGH 538 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.9162 11.2481 7.3057 REMARK 3 T TENSOR REMARK 3 T11: 0.1260 T22: 0.1339 REMARK 3 T33: 0.0965 T12: 0.0138 REMARK 3 T13: 0.0096 T23: 0.0170 REMARK 3 L TENSOR REMARK 3 L11: 6.1921 L22: 4.0923 REMARK 3 L33: 5.3699 L12: 0.6781 REMARK 3 L13: 1.1835 L23: -0.7450 REMARK 3 S TENSOR REMARK 3 S11: 0.0633 S12: 0.3987 S13: 0.1783 REMARK 3 S21: -0.0389 S22: -0.0502 S23: -0.2372 REMARK 3 S31: -0.0989 S32: 0.2918 S33: 0.0111 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 539 THROUGH 548 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.8090 12.0586 8.4688 REMARK 3 T TENSOR REMARK 3 T11: 0.1183 T22: 0.1316 REMARK 3 T33: 0.1102 T12: -0.0038 REMARK 3 T13: -0.0108 T23: 0.0283 REMARK 3 L TENSOR REMARK 3 L11: 4.3894 L22: 4.7256 REMARK 3 L33: 2.3708 L12: -0.9887 REMARK 3 L13: 1.2424 L23: 1.7208 REMARK 3 S TENSOR REMARK 3 S11: 0.1279 S12: 0.1070 S13: 0.0982 REMARK 3 S21: -0.1734 S22: -0.0716 S23: 0.2604 REMARK 3 S31: 0.0861 S32: -0.2487 S33: -0.0564 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 549 THROUGH 555 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.2334 19.8378 5.0226 REMARK 3 T TENSOR REMARK 3 T11: 0.2115 T22: 0.1609 REMARK 3 T33: 0.1952 T12: -0.0003 REMARK 3 T13: 0.0142 T23: 0.0534 REMARK 3 L TENSOR REMARK 3 L11: 4.4192 L22: 1.7264 REMARK 3 L33: 8.9246 L12: 0.9096 REMARK 3 L13: 6.2183 L23: 1.7025 REMARK 3 S TENSOR REMARK 3 S11: -0.2711 S12: 0.1245 S13: 0.3632 REMARK 3 S21: -0.2687 S22: 0.0109 S23: -0.2531 REMARK 3 S31: -0.6149 S32: 0.1464 S33: 0.2642 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 556 THROUGH 560 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.1894 8.2673 3.5574 REMARK 3 T TENSOR REMARK 3 T11: 0.2497 T22: 0.1450 REMARK 3 T33: 0.1114 T12: 0.0542 REMARK 3 T13: -0.0586 T23: -0.0112 REMARK 3 L TENSOR REMARK 3 L11: 6.6421 L22: 4.3344 REMARK 3 L33: 6.4312 L12: 2.7686 REMARK 3 L13: -2.5301 L23: -5.2253 REMARK 3 S TENSOR REMARK 3 S11: 0.0357 S12: 0.2777 S13: -0.2377 REMARK 3 S21: -0.4710 S22: 0.0062 S23: -0.1475 REMARK 3 S31: 0.8883 S32: 0.1085 S33: -0.0810 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 561 THROUGH 573 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.5395 13.1762 8.2296 REMARK 3 T TENSOR REMARK 3 T11: 0.1458 T22: 0.1738 REMARK 3 T33: 0.1767 T12: -0.0165 REMARK 3 T13: -0.0178 T23: 0.0141 REMARK 3 L TENSOR REMARK 3 L11: 4.3170 L22: 4.3940 REMARK 3 L33: 6.5312 L12: -2.5226 REMARK 3 L13: 2.0210 L23: -2.3753 REMARK 3 S TENSOR REMARK 3 S11: 0.1364 S12: -0.0789 S13: -0.1001 REMARK 3 S21: -0.2237 S22: 0.0919 S23: 0.3761 REMARK 3 S31: 0.1930 S32: -0.4175 S33: -0.2399 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 574 THROUGH 580 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.8324 25.4258 6.9829 REMARK 3 T TENSOR REMARK 3 T11: 0.4208 T22: 0.4764 REMARK 3 T33: 0.4796 T12: 0.0419 REMARK 3 T13: 0.0628 T23: 0.1405 REMARK 3 L TENSOR REMARK 3 L11: 0.9869 L22: 0.9025 REMARK 3 L33: 7.7713 L12: -0.6334 REMARK 3 L13: 0.4698 L23: 1.6322 REMARK 3 S TENSOR REMARK 3 S11: 0.1776 S12: 0.1420 S13: 0.7818 REMARK 3 S21: -1.2478 S22: -0.2863 S23: -0.4741 REMARK 3 S31: -1.0180 S32: 0.7334 S33: -0.0745 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.1692 -8.2703 13.8219 REMARK 3 T TENSOR REMARK 3 T11: 0.2158 T22: 0.1630 REMARK 3 T33: 0.2825 T12: -0.0344 REMARK 3 T13: 0.0177 T23: -0.0099 REMARK 3 L TENSOR REMARK 3 L11: 0.8671 L22: 3.0846 REMARK 3 L33: 3.0575 L12: 0.9272 REMARK 3 L13: -0.1055 L23: -1.3707 REMARK 3 S TENSOR REMARK 3 S11: -0.2906 S12: 0.2325 S13: -0.4928 REMARK 3 S21: -0.4437 S22: 0.2056 S23: 0.0501 REMARK 3 S31: 0.5880 S32: -0.2762 S33: 0.1519 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 1 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.9730 -9.9898 16.5287 REMARK 3 T TENSOR REMARK 3 T11: 0.2816 T22: 0.1844 REMARK 3 T33: 0.3253 T12: -0.0621 REMARK 3 T13: -0.0373 T23: 0.1037 REMARK 3 L TENSOR REMARK 3 L11: 4.8715 L22: 1.6413 REMARK 3 L33: 1.3961 L12: 0.3596 REMARK 3 L13: 0.4272 L23: 0.3788 REMARK 3 S TENSOR REMARK 3 S11: -0.1781 S12: 0.0831 S13: -0.0641 REMARK 3 S21: -0.4198 S22: 0.3362 S23: 0.5416 REMARK 3 S31: 0.4838 S32: -0.2357 S33: -0.0208 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 7KZG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1000253277. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-OCT-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : SI(111) AND SI(220) DOUBLE REMARK 200 CRYSTAL 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 : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28121 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680 REMARK 200 RESOLUTION RANGE LOW (A) : 37.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.30 REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 4DK9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG1000, HEPES, PH 7.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 20.73250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.36650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.20700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.36650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.73250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.20700 REMARK 290 SMTRY3 4 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: 4780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D 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 MET A 407 REMARK 465 GLY A 408 REMARK 465 SER A 409 REMARK 465 SER A 410 REMARK 465 HIS A 411 REMARK 465 HIS A 412 REMARK 465 HIS A 413 REMARK 465 HIS A 414 REMARK 465 HIS A 415 REMARK 465 HIS A 416 REMARK 465 SER A 417 REMARK 465 SER A 418 REMARK 465 GLY A 419 REMARK 465 LEU A 420 REMARK 465 VAL A 421 REMARK 465 PRO A 422 REMARK 465 ARG A 423 REMARK 465 GLY A 424 REMARK 465 SER A 425 REMARK 465 ALA A 426 REMARK 465 LEU A 427 REMARK 465 SER A 428 REMARK 465 PRO A 429 REMARK 465 PRO A 430 REMARK 465 ARG A 431 REMARK 465 ARG A 432 REMARK 465 LYS A 433 REMARK 465 ALA A 434 REMARK 465 PHE A 435 REMARK 465 LYS A 436 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 LYS A 472 CE NZ REMARK 470 LYS A 480 CE NZ REMARK 470 LYS A 484 CE NZ REMARK 470 HIS A 561 ND1 CD2 CE1 NE2 REMARK 470 LYS A 576 CD CE NZ REMARK 470 SER A 578 OG REMARK 470 SER A 580 OG 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 DG C 6 C3' - O3' - P ANGL. DEV. = 9.4 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 ASN A 551 46.94 -88.48 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 NA A 705 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE A 532 O REMARK 620 2 LEU A 534 O 102.1 REMARK 620 3 ILE A 537 O 94.3 97.1 REMARK 620 4 HOH A 927 O 89.8 84.0 175.4 REMARK 620 5 DA C 10 OP1 168.9 88.5 87.6 87.9 REMARK 620 6 HOH C 211 O 87.4 165.0 93.8 84.4 81.5 REMARK 620 N 1 2 3 4 5 DBREF 7KZG A 426 580 UNP O95243 MBD4_HUMAN 426 580 DBREF 7KZG C 1 12 PDB 7KZG 7KZG 1 12 DBREF 7KZG D 1 12 PDB 7KZG 7KZG 1 12 SEQADV 7KZG MET A 407 UNP O95243 EXPRESSION TAG SEQADV 7KZG GLY A 408 UNP O95243 EXPRESSION TAG SEQADV 7KZG SER A 409 UNP O95243 EXPRESSION TAG SEQADV 7KZG SER A 410 UNP O95243 EXPRESSION TAG SEQADV 7KZG HIS A 411 UNP O95243 EXPRESSION TAG SEQADV 7KZG HIS A 412 UNP O95243 EXPRESSION TAG SEQADV 7KZG HIS A 413 UNP O95243 EXPRESSION TAG SEQADV 7KZG HIS A 414 UNP O95243 EXPRESSION TAG SEQADV 7KZG HIS A 415 UNP O95243 EXPRESSION TAG SEQADV 7KZG HIS A 416 UNP O95243 EXPRESSION TAG SEQADV 7KZG SER A 417 UNP O95243 EXPRESSION TAG SEQADV 7KZG SER A 418 UNP O95243 EXPRESSION TAG SEQADV 7KZG GLY A 419 UNP O95243 EXPRESSION TAG SEQADV 7KZG LEU A 420 UNP O95243 EXPRESSION TAG SEQADV 7KZG VAL A 421 UNP O95243 EXPRESSION TAG SEQADV 7KZG PRO A 422 UNP O95243 EXPRESSION TAG SEQADV 7KZG ARG A 423 UNP O95243 EXPRESSION TAG SEQADV 7KZG GLY A 424 UNP O95243 EXPRESSION TAG SEQADV 7KZG SER A 425 UNP O95243 EXPRESSION TAG SEQRES 1 A 174 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 174 LEU VAL PRO ARG GLY SER ALA LEU SER PRO PRO ARG ARG SEQRES 3 A 174 LYS ALA PHE LYS LYS TRP THR PRO PRO ARG SER PRO PHE SEQRES 4 A 174 ASN LEU VAL GLN GLU THR LEU PHE HIS ASP PRO TRP LYS SEQRES 5 A 174 LEU LEU ILE ALA THR ILE PHE LEU ASN ARG THR SER GLY SEQRES 6 A 174 LYS MET ALA ILE PRO VAL LEU TRP LYS PHE LEU GLU LYS SEQRES 7 A 174 TYR PRO SER ALA GLU VAL ALA ARG THR ALA ASP TRP ARG SEQRES 8 A 174 ASP VAL SER GLU LEU LEU LYS PRO LEU GLY LEU TYR ASP SEQRES 9 A 174 LEU ARG ALA LYS THR ILE VAL LYS PHE SER ASP GLU TYR SEQRES 10 A 174 LEU THR LYS GLN TRP LYS TYR PRO ILE GLU LEU HIS GLY SEQRES 11 A 174 ILE GLY LYS TYR GLY ASN ASP SER TYR ARG ILE PHE CYS SEQRES 12 A 174 VAL ASN GLU TRP LYS GLN VAL HIS PRO GLU ASP HIS LYS SEQRES 13 A 174 LEU ASN LYS TYR HIS ASP TRP LEU TRP GLU ASN HIS GLU SEQRES 14 A 174 LYS LEU SER LEU SER SEQRES 1 C 12 DC DC DA DG DC DG NR1 DG DC DA DG DC SEQRES 1 D 12 DG DC DT DG DC DG DC DG DC DT DG DG HET NR1 C 7 11 HET GOL A 701 6 HET PEG A 702 7 HET EDO A 703 4 HET GOL A 704 6 HET NA A 705 1 HET CL A 706 1 HET GOL C 101 6 HET GOL D 101 6 HETNAM NR1 (3R,4R)-3-HYDROXY-4-[(PHOSPHONOOXY)METHYL]PYRROLIDINIUM HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM EDO 1,2-ETHANEDIOL HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 NR1 C5 H13 N O5 P 1+ FORMUL 4 GOL 4(C3 H8 O3) FORMUL 5 PEG C4 H10 O3 FORMUL 6 EDO C2 H6 O2 FORMUL 8 NA NA 1+ FORMUL 9 CL CL 1- FORMUL 12 HOH *235(H2 O) HELIX 1 AA1 VAL A 448 PHE A 453 1 6 HELIX 2 AA2 ASP A 455 LEU A 466 1 12 HELIX 3 AA3 SER A 470 TYR A 485 1 16 HELIX 4 AA4 SER A 487 ARG A 492 1 6 HELIX 5 AA5 ASP A 495 LYS A 504 1 10 HELIX 6 AA6 PRO A 505 GLY A 507 5 3 HELIX 7 AA7 LEU A 508 LYS A 526 1 19 HELIX 8 AA8 TYR A 530 LEU A 534 5 5 HELIX 9 AA9 GLY A 538 CYS A 549 1 12 HELIX 10 AB1 GLU A 552 VAL A 556 5 5 HELIX 11 AB2 ASP A 560 HIS A 574 1 15 LINK O3' DG C 6 P NR1 C 7 1555 1555 1.56 LINK O3' NR1 C 7 P DG C 8 1555 1555 1.56 LINK O ILE A 532 NA NA A 705 1555 1555 2.39 LINK O LEU A 534 NA NA A 705 1555 1555 2.38 LINK O ILE A 537 NA NA A 705 1555 1555 2.37 LINK NA NA A 705 O HOH A 927 1555 1555 2.56 LINK NA NA A 705 OP1 DA C 10 1555 1555 2.68 LINK NA NA A 705 O HOH C 211 1555 1555 2.42 CRYST1 41.465 56.414 102.733 90.00 90.00 90.00 P 21 21 21 4 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 0.024117 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017726 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009734 0.00000