HEADER HYDROLASE/DNA 09-DEC-20 7KZ0 TITLE HUMAN MBD4 GLYCOSYLASE DOMAIN BOUND TO DNA CONTAINING SUBSTRATE ANALOG TITLE 2 2'-DEOXY-PSEUDOURIDINE 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*(P2U)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: 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 MBD4, PROTEIN-DNA COMPLEX, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.S.PIDUGU,E.POZHARSKI,A.C.DROHAT REVDAT 2 18-OCT-23 7KZ0 1 REMARK REVDAT 1 10-NOV-21 7KZ0 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. 1.57 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) : 1.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 35292 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1766 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 38.6500 - 3.6900 1.00 2790 137 0.1549 0.1600 REMARK 3 2 3.6900 - 2.9300 0.99 2635 125 0.1426 0.1599 REMARK 3 3 2.9300 - 2.5600 1.00 2632 139 0.1660 0.2137 REMARK 3 4 2.5600 - 2.3300 1.00 2601 126 0.1762 0.2303 REMARK 3 5 2.3300 - 2.1600 0.99 2571 121 0.1988 0.1862 REMARK 3 6 2.1600 - 2.0300 0.99 2531 148 0.2128 0.2724 REMARK 3 7 2.0300 - 1.9300 1.00 2566 142 0.2097 0.2522 REMARK 3 8 1.9300 - 1.8500 0.98 2538 121 0.3122 0.3516 REMARK 3 9 1.8500 - 1.7700 1.00 2544 148 0.2385 0.2761 REMARK 3 10 1.7700 - 1.7100 0.99 2510 156 0.2729 0.3005 REMARK 3 11 1.7100 - 1.6600 1.00 2550 137 0.2880 0.3109 REMARK 3 12 1.6600 - 1.6100 1.00 2563 132 0.2906 0.2906 REMARK 3 13 1.6100 - 1.5700 0.98 2495 134 0.3210 0.3666 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.40 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 : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 437:474) REMARK 3 ORIGIN FOR THE GROUP (A): 8.7194 20.9404 18.8345 REMARK 3 T TENSOR REMARK 3 T11: 0.1216 T22: 0.1608 REMARK 3 T33: 0.1190 T12: -0.0033 REMARK 3 T13: -0.0018 T23: -0.0073 REMARK 3 L TENSOR REMARK 3 L11: 3.1417 L22: 3.4840 REMARK 3 L33: 1.4612 L12: -0.9829 REMARK 3 L13: 0.3847 L23: 0.2364 REMARK 3 S TENSOR REMARK 3 S11: -0.0913 S12: -0.1005 S13: 0.2473 REMARK 3 S21: 0.0512 S22: 0.0765 S23: 0.0551 REMARK 3 S31: -0.1237 S32: 0.0076 S33: 0.0083 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 475:525) REMARK 3 ORIGIN FOR THE GROUP (A): 21.8062 13.3580 23.8616 REMARK 3 T TENSOR REMARK 3 T11: 0.1526 T22: 0.2018 REMARK 3 T33: 0.1344 T12: 0.0290 REMARK 3 T13: -0.0238 T23: -0.0210 REMARK 3 L TENSOR REMARK 3 L11: 3.2822 L22: 3.5264 REMARK 3 L33: 1.4728 L12: 1.6915 REMARK 3 L13: -0.7785 L23: -0.6084 REMARK 3 S TENSOR REMARK 3 S11: -0.0173 S12: -0.1920 S13: 0.0039 REMARK 3 S21: 0.2298 S22: 0.0739 S23: -0.2105 REMARK 3 S31: 0.0296 S32: 0.1576 S33: -0.0499 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 526:580) REMARK 3 ORIGIN FOR THE GROUP (A): 7.7334 23.3164 7.8470 REMARK 3 T TENSOR REMARK 3 T11: 0.1826 T22: 0.1698 REMARK 3 T33: 0.1292 T12: -0.0246 REMARK 3 T13: -0.0079 T23: 0.0156 REMARK 3 L TENSOR REMARK 3 L11: 8.2043 L22: 2.4657 REMARK 3 L33: 1.7591 L12: -2.0811 REMARK 3 L13: 0.5928 L23: -0.3572 REMARK 3 S TENSOR REMARK 3 S11: 0.0206 S12: 0.3110 S13: 0.2815 REMARK 3 S21: -0.1524 S22: -0.0103 S23: 0.0623 REMARK 3 S31: -0.1120 S32: -0.0313 S33: -0.0178 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN C AND RESID 1:4) REMARK 3 ORIGIN FOR THE GROUP (A): -0.0067 -7.8088 21.7244 REMARK 3 T TENSOR REMARK 3 T11: 0.4813 T22: 0.3588 REMARK 3 T33: 0.4573 T12: -0.0081 REMARK 3 T13: 0.1317 T23: 0.0528 REMARK 3 L TENSOR REMARK 3 L11: 5.9692 L22: 7.5805 REMARK 3 L33: 5.5475 L12: 5.8761 REMARK 3 L13: -5.6074 L23: -6.2447 REMARK 3 S TENSOR REMARK 3 S11: -0.5477 S12: -0.4150 S13: -0.1991 REMARK 3 S21: -1.5507 S22: 0.0335 S23: -0.8047 REMARK 3 S31: 1.4726 S32: 1.3230 S33: 0.9737 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN C AND RESID 5:8) REMARK 3 ORIGIN FOR THE GROUP (A): 5.7362 6.4371 15.7585 REMARK 3 T TENSOR REMARK 3 T11: 0.1592 T22: 0.2117 REMARK 3 T33: 0.2100 T12: -0.0583 REMARK 3 T13: -0.0378 T23: 0.0132 REMARK 3 L TENSOR REMARK 3 L11: 1.1074 L22: 5.4319 REMARK 3 L33: 3.4275 L12: -0.8059 REMARK 3 L13: -1.2207 L23: -1.9031 REMARK 3 S TENSOR REMARK 3 S11: -0.0721 S12: 0.0017 S13: -0.1130 REMARK 3 S21: -0.1379 S22: 0.2768 S23: 0.5422 REMARK 3 S31: 0.2817 S32: -0.4812 S33: -0.1655 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN C AND RESID 9:12) REMARK 3 ORIGIN FOR THE GROUP (A): 20.3644 4.6115 7.1694 REMARK 3 T TENSOR REMARK 3 T11: 0.2353 T22: 0.3100 REMARK 3 T33: 0.2296 T12: 0.0444 REMARK 3 T13: 0.0140 T23: -0.0823 REMARK 3 L TENSOR REMARK 3 L11: 3.1649 L22: 9.0569 REMARK 3 L33: 2.7935 L12: 1.3599 REMARK 3 L13: -1.9459 L23: 2.7324 REMARK 3 S TENSOR REMARK 3 S11: -0.2041 S12: 0.4284 S13: -0.2743 REMARK 3 S21: -0.0366 S22: 0.4434 S23: -0.9210 REMARK 3 S31: 0.4461 S32: 0.5787 S33: -0.1181 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN D AND RESID 1:4) REMARK 3 ORIGIN FOR THE GROUP (A): 14.7020 -2.2124 5.2713 REMARK 3 T TENSOR REMARK 3 T11: 0.4637 T22: 0.4397 REMARK 3 T33: 0.3236 T12: -0.0253 REMARK 3 T13: 0.0425 T23: 0.0904 REMARK 3 L TENSOR REMARK 3 L11: 3.5795 L22: 2.3956 REMARK 3 L33: 3.5753 L12: 0.5214 REMARK 3 L13: 3.3243 L23: -0.4436 REMARK 3 S TENSOR REMARK 3 S11: 0.4151 S12: 0.2648 S13: -0.0623 REMARK 3 S21: 0.2102 S22: 0.6601 S23: 0.6405 REMARK 3 S31: 0.8088 S32: -0.9740 S33: -0.9665 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN D AND RESID 5:8) REMARK 3 ORIGIN FOR THE GROUP (A): 12.4799 -0.1646 21.9778 REMARK 3 T TENSOR REMARK 3 T11: 0.1548 T22: 0.1494 REMARK 3 T33: 0.1581 T12: 0.0058 REMARK 3 T13: -0.0061 T23: -0.0021 REMARK 3 L TENSOR REMARK 3 L11: 9.3622 L22: 6.1324 REMARK 3 L33: 3.1794 L12: 1.4972 REMARK 3 L13: -2.7138 L23: -4.2295 REMARK 3 S TENSOR REMARK 3 S11: -0.3626 S12: -0.2335 S13: -0.0942 REMARK 3 S21: -0.0973 S22: 0.3275 S23: 0.3425 REMARK 3 S31: 0.3729 S32: -0.0768 S33: 0.0970 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN D AND RESID 9:12) REMARK 3 ORIGIN FOR THE GROUP (A): -3.8938 -0.1983 24.6827 REMARK 3 T TENSOR REMARK 3 T11: 0.2113 T22: 0.3950 REMARK 3 T33: 0.5142 T12: -0.0310 REMARK 3 T13: 0.0018 T23: 0.0373 REMARK 3 L TENSOR REMARK 3 L11: 6.8728 L22: 4.0718 REMARK 3 L33: 9.1424 L12: 5.2446 REMARK 3 L13: 6.4098 L23: 4.3107 REMARK 3 S TENSOR REMARK 3 S11: -0.6354 S12: -0.9468 S13: 1.2590 REMARK 3 S21: -0.8436 S22: 0.0918 S23: 0.7377 REMARK 3 S31: -0.0811 S32: -0.0413 S33: 0.5370 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 7KZ0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1000253345. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 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 : 35493 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.570 REMARK 200 RESOLUTION RANGE LOW (A) : 38.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 26.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 24.50 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 (%): 44.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, POTASSIUM SODIUM TARTRATE, PH REMARK 280 7.4, VAPOR 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 20.68050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.70800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.43000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.70800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.68050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.43000 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: 4590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 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 A 873 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH A 874 DISTANCE = 6.93 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 K A 602 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE A 532 O REMARK 620 2 LEU A 534 O 94.5 REMARK 620 3 ILE A 537 O 88.7 88.0 REMARK 620 4 HOH A 834 O 97.9 84.6 170.4 REMARK 620 5 DA C 10 OP1 174.9 88.4 87.2 86.5 REMARK 620 6 HOH C 110 O 93.3 168.5 83.8 102.6 83.2 REMARK 620 N 1 2 3 4 5 DBREF 7KZ0 A 426 580 UNP O95243 MBD4_HUMAN 426 580 DBREF 7KZ0 C 1 12 PDB 7KZ0 7KZ0 1 12 DBREF 7KZ0 D 1 12 PDB 7KZ0 7KZ0 1 12 SEQADV 7KZ0 MET A 407 UNP O95243 EXPRESSION TAG SEQADV 7KZ0 GLY A 408 UNP O95243 EXPRESSION TAG SEQADV 7KZ0 SER A 409 UNP O95243 EXPRESSION TAG SEQADV 7KZ0 SER A 410 UNP O95243 EXPRESSION TAG SEQADV 7KZ0 HIS A 411 UNP O95243 EXPRESSION TAG SEQADV 7KZ0 HIS A 412 UNP O95243 EXPRESSION TAG SEQADV 7KZ0 HIS A 413 UNP O95243 EXPRESSION TAG SEQADV 7KZ0 HIS A 414 UNP O95243 EXPRESSION TAG SEQADV 7KZ0 HIS A 415 UNP O95243 EXPRESSION TAG SEQADV 7KZ0 HIS A 416 UNP O95243 EXPRESSION TAG SEQADV 7KZ0 SER A 417 UNP O95243 EXPRESSION TAG SEQADV 7KZ0 SER A 418 UNP O95243 EXPRESSION TAG SEQADV 7KZ0 GLY A 419 UNP O95243 EXPRESSION TAG SEQADV 7KZ0 LEU A 420 UNP O95243 EXPRESSION TAG SEQADV 7KZ0 VAL A 421 UNP O95243 EXPRESSION TAG SEQADV 7KZ0 PRO A 422 UNP O95243 EXPRESSION TAG SEQADV 7KZ0 ARG A 423 UNP O95243 EXPRESSION TAG SEQADV 7KZ0 GLY A 424 UNP O95243 EXPRESSION TAG SEQADV 7KZ0 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 P2U DG DC DA DG DC SEQRES 1 D 12 DG DC DT DG DC DG DC DG DC DT DG DG HET P2U C 7 19 HET GOL A 601 6 HET K A 602 1 HET GOL A 603 6 HET GOL D 101 6 HETNAM P2U 2'-DEOXY-PSEUDOURIDINE-5'MONOPHOSPHATE HETNAM GOL GLYCEROL HETNAM K POTASSIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 P2U C9 H13 N2 O8 P FORMUL 4 GOL 3(C3 H8 O3) FORMUL 5 K K 1+ FORMUL 8 HOH *263(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 P2U C 7 1555 1555 1.60 LINK O3' P2U C 7 P DG C 8 1555 1555 1.61 LINK O ILE A 532 K K A 602 1555 1555 2.66 LINK O LEU A 534 K K A 602 1555 1555 2.61 LINK O ILE A 537 K K A 602 1555 1555 2.62 LINK K K A 602 O HOH A 834 1555 1555 2.76 LINK K K A 602 OP1 DA C 10 1555 1555 2.78 LINK K K A 602 O HOH C 110 1555 1555 2.71 CRYST1 41.361 56.860 105.416 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 0.024177 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017587 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009486 0.00000