HEADER HYDROLASE/DNA 09-DEC-20 7KZ1 TITLE HUMAN MBD4 GLYCOSYLASE DOMAIN BOUND TO DNA CONTAINING AN ABASIC SITE 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*(ORP)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 PROTEIN-DNA COMPLEX, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.S.PIDUGU,H.BRIGHT,E.POZHARSKI,A.C.DROHAT REVDAT 2 18-OCT-23 7KZ1 1 REMARK REVDAT 1 10-NOV-21 7KZ1 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. 1.62 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) : 1.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 28206 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 1376 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 37.6100 - 3.4900 1.00 2880 155 0.1548 0.1583 REMARK 3 2 3.4900 - 2.7700 1.00 2757 133 0.1659 0.2033 REMARK 3 3 2.7700 - 2.4200 1.00 2702 145 0.1815 0.2097 REMARK 3 4 2.4200 - 2.2000 1.00 2695 146 0.1814 0.2272 REMARK 3 5 2.2000 - 2.0400 1.00 2665 142 0.1871 0.2358 REMARK 3 6 2.0400 - 1.9200 1.00 2673 129 0.2069 0.2353 REMARK 3 7 1.9200 - 1.8300 1.00 2657 139 0.2268 0.2856 REMARK 3 8 1.8300 - 1.7500 1.00 2651 140 0.2525 0.2591 REMARK 3 9 1.7500 - 1.6800 1.00 2662 123 0.2926 0.3245 REMARK 3 10 1.6800 - 1.6200 0.94 2488 124 0.3196 0.3433 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.960 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.21 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 : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 436 THROUGH 455 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.2846 -16.4038 17.3377 REMARK 3 T TENSOR REMARK 3 T11: 0.1761 T22: 0.2809 REMARK 3 T33: 0.2966 T12: 0.0524 REMARK 3 T13: -0.0229 T23: 0.0491 REMARK 3 L TENSOR REMARK 3 L11: 4.4561 L22: 3.4833 REMARK 3 L33: 3.9836 L12: -1.1495 REMARK 3 L13: -3.0834 L23: -1.6444 REMARK 3 S TENSOR REMARK 3 S11: -0.0567 S12: -0.3948 S13: -0.6084 REMARK 3 S21: -0.0226 S22: -0.1168 S23: -0.2325 REMARK 3 S31: 0.4361 S32: 0.6040 S33: 0.0294 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 456 THROUGH 525 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.8529 -1.6560 20.7562 REMARK 3 T TENSOR REMARK 3 T11: 0.1415 T22: 0.1463 REMARK 3 T33: 0.1085 T12: -0.0061 REMARK 3 T13: 0.0071 T23: -0.0352 REMARK 3 L TENSOR REMARK 3 L11: 2.7485 L22: 3.1597 REMARK 3 L33: 2.1823 L12: 0.7224 REMARK 3 L13: -0.2423 L23: 0.1854 REMARK 3 S TENSOR REMARK 3 S11: 0.1364 S12: -0.2413 S13: 0.2219 REMARK 3 S21: 0.3046 S22: -0.1388 S23: 0.1241 REMARK 3 S31: -0.1276 S32: -0.0734 S33: 0.0102 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 526 THROUGH 538 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.5791 -10.3128 6.9859 REMARK 3 T TENSOR REMARK 3 T11: 0.2238 T22: 0.2349 REMARK 3 T33: 0.2026 T12: 0.0156 REMARK 3 T13: -0.0455 T23: -0.0606 REMARK 3 L TENSOR REMARK 3 L11: 5.4653 L22: 7.3719 REMARK 3 L33: 2.4683 L12: 0.2404 REMARK 3 L13: -2.0065 L23: 1.1564 REMARK 3 S TENSOR REMARK 3 S11: 0.1108 S12: 0.5329 S13: -0.2805 REMARK 3 S21: -0.2099 S22: -0.1508 S23: 0.5288 REMARK 3 S31: 0.1473 S32: -0.4381 S33: 0.0254 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 539 THROUGH 560 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.6020 -12.7497 6.1080 REMARK 3 T TENSOR REMARK 3 T11: 0.1909 T22: 0.1953 REMARK 3 T33: 0.1190 T12: 0.0200 REMARK 3 T13: -0.0250 T23: -0.0498 REMARK 3 L TENSOR REMARK 3 L11: 6.0953 L22: 4.3614 REMARK 3 L33: 4.7921 L12: -0.9677 REMARK 3 L13: -2.3625 L23: -1.6742 REMARK 3 S TENSOR REMARK 3 S11: 0.1281 S12: 0.2728 S13: -0.2645 REMARK 3 S21: -0.4707 S22: -0.1416 S23: -0.0189 REMARK 3 S31: 0.1697 S32: 0.0187 S33: -0.0081 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 561 THROUGH 573 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.7248 -12.6023 8.2031 REMARK 3 T TENSOR REMARK 3 T11: 0.1731 T22: 0.3471 REMARK 3 T33: 0.3061 T12: 0.0179 REMARK 3 T13: 0.0419 T23: -0.0114 REMARK 3 L TENSOR REMARK 3 L11: 7.2456 L22: 3.8408 REMARK 3 L33: 8.0933 L12: -4.0739 REMARK 3 L13: -0.8429 L23: 3.4549 REMARK 3 S TENSOR REMARK 3 S11: 0.1111 S12: -0.2471 S13: 0.0624 REMARK 3 S21: -0.5971 S22: 0.2385 S23: -0.9031 REMARK 3 S31: 0.0250 S32: 0.7205 S33: -0.3747 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 574 THROUGH 580 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.0534 -22.2892 11.4891 REMARK 3 T TENSOR REMARK 3 T11: 0.5552 T22: 0.5067 REMARK 3 T33: 0.7802 T12: 0.1712 REMARK 3 T13: -0.2499 T23: -0.2422 REMARK 3 L TENSOR REMARK 3 L11: 6.3488 L22: 2.3546 REMARK 3 L33: 6.9454 L12: -0.7978 REMARK 3 L13: -4.2240 L23: -1.4222 REMARK 3 S TENSOR REMARK 3 S11: -0.5939 S12: 0.4036 S13: -2.5094 REMARK 3 S21: -0.1949 S22: -0.8068 S23: 0.5229 REMARK 3 S31: 1.5406 S32: 0.9261 S33: 1.5729 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.0259 10.0425 11.5577 REMARK 3 T TENSOR REMARK 3 T11: 0.3424 T22: 0.2389 REMARK 3 T33: 0.6179 T12: -0.0246 REMARK 3 T13: -0.0963 T23: -0.0019 REMARK 3 L TENSOR REMARK 3 L11: 0.2594 L22: 2.9954 REMARK 3 L33: 4.7808 L12: 0.5974 REMARK 3 L13: -0.1690 L23: 2.2725 REMARK 3 S TENSOR REMARK 3 S11: -0.5724 S12: 0.3505 S13: 0.8903 REMARK 3 S21: -0.8488 S22: 0.5193 S23: -0.4933 REMARK 3 S31: -0.8918 S32: 0.4474 S33: 0.2190 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 1 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.7223 11.8216 13.7187 REMARK 3 T TENSOR REMARK 3 T11: 0.3948 T22: 0.1876 REMARK 3 T33: 0.5140 T12: -0.0539 REMARK 3 T13: 0.0543 T23: -0.1115 REMARK 3 L TENSOR REMARK 3 L11: 8.2558 L22: 2.8354 REMARK 3 L33: 4.8128 L12: 1.6015 REMARK 3 L13: 1.6787 L23: -1.3921 REMARK 3 S TENSOR REMARK 3 S11: -0.1990 S12: 0.2461 S13: 0.1258 REMARK 3 S21: -0.6009 S22: 0.2325 S23: -0.6513 REMARK 3 S31: -0.3909 S32: 0.4339 S33: -0.1132 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 7KZ1 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_1000253298. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-NOV-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : LIQUID NITROGEN-COOLED DOUBLE REMARK 200 CRYSTAL SI(111) 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 : 28461 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.620 REMARK 200 RESOLUTION RANGE LOW (A) : 37.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 12.00 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 (%): 41.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG400, TRIS-HCL, PH 8.0, 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 20.33450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.38350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.14600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.38350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.33450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.14600 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: 4070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 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 LEU A 579 REMARK 465 SER A 580 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 437 CD CE NZ REMARK 470 LYS A 472 CE NZ REMARK 470 LYS A 480 CE NZ REMARK 470 GLU A 483 CD OE1 OE2 REMARK 470 LYS A 484 CD CE NZ REMARK 470 LYS A 526 CE NZ REMARK 470 HIS A 561 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 575 CG CD OE1 OE2 REMARK 470 LYS A 576 CG CD CE NZ REMARK 470 SER A 578 OG 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 O HOH A 885 O HOH A 895 2.17 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 703 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE A 532 O REMARK 620 2 LEU A 534 O 100.9 REMARK 620 3 ILE A 537 O 91.8 96.5 REMARK 620 4 HOH A 866 O 92.1 84.8 175.6 REMARK 620 5 DA C 10 OP1 171.1 87.8 88.9 86.9 REMARK 620 6 HOH C 109 O 86.3 171.3 88.1 90.1 84.9 REMARK 620 N 1 2 3 4 5 DBREF 7KZ1 A 426 580 UNP O95243 MBD4_HUMAN 426 580 DBREF 7KZ1 C 1 12 PDB 7KZ1 7KZ1 1 12 DBREF 7KZ1 D 1 12 PDB 7KZ1 7KZ1 1 12 SEQADV 7KZ1 GLY A 424 UNP O95243 EXPRESSION TAG SEQADV 7KZ1 SER A 425 UNP O95243 EXPRESSION TAG SEQRES 1 A 157 GLY SER ALA LEU SER PRO PRO ARG ARG LYS ALA PHE LYS SEQRES 2 A 157 LYS TRP THR PRO PRO ARG SER PRO PHE ASN LEU VAL GLN SEQRES 3 A 157 GLU THR LEU PHE HIS ASP PRO TRP LYS LEU LEU ILE ALA SEQRES 4 A 157 THR ILE PHE LEU ASN ARG THR SER GLY LYS MET ALA ILE SEQRES 5 A 157 PRO VAL LEU TRP LYS PHE LEU GLU LYS TYR PRO SER ALA SEQRES 6 A 157 GLU VAL ALA ARG THR ALA ASP TRP ARG ASP VAL SER GLU SEQRES 7 A 157 LEU LEU LYS PRO LEU GLY LEU TYR ASP LEU ARG ALA LYS SEQRES 8 A 157 THR ILE VAL LYS PHE SER ASP GLU TYR LEU THR LYS GLN SEQRES 9 A 157 TRP LYS TYR PRO ILE GLU LEU HIS GLY ILE GLY LYS TYR SEQRES 10 A 157 GLY ASN ASP SER TYR ARG ILE PHE CYS VAL ASN GLU TRP SEQRES 11 A 157 LYS GLN VAL HIS PRO GLU ASP HIS LYS LEU ASN LYS TYR SEQRES 12 A 157 HIS ASP TRP LEU TRP GLU ASN HIS GLU LYS LEU SER LEU SEQRES 13 A 157 SER SEQRES 1 C 12 DC DC DA DG DC DG ORP DG DC DA DG DC SEQRES 1 D 12 DG DC DT DG DC DG DC DG DC DT DG DG HET ORP C 7 12 HET GOL A 701 6 HET EDO A 702 4 HET NA A 703 1 HETNAM ORP 2-DEOXY-5-PHOSPHONO-RIBOSE HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETNAM NA SODIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ORP C5 H11 O7 P FORMUL 4 GOL C3 H8 O3 FORMUL 5 EDO C2 H6 O2 FORMUL 6 NA NA 1+ FORMUL 7 HOH *152(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 SER A 578 1 19 LINK O3' DG C 6 P ORP C 7 1555 1555 1.55 LINK O3 ORP C 7 P DG C 8 1555 1555 1.56 LINK O ILE A 532 NA NA A 703 1555 1555 2.45 LINK O LEU A 534 NA NA A 703 1555 1555 2.35 LINK O ILE A 537 NA NA A 703 1555 1555 2.40 LINK NA NA A 703 O HOH A 866 1555 1555 2.31 LINK NA NA A 703 OP1 DA C 10 1555 1555 2.70 LINK NA NA A 703 O HOH C 109 1555 1555 2.56 CRYST1 40.669 54.292 98.767 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 0.024589 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018419 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010125 0.00000