HEADER TRANSCRIPTION/DNA 08-MAR-18 6CNQ TITLE MBD2 IN COMPLEX WITH METHYLATED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYL-CPG-BINDING DOMAIN PROTEIN 2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 143-220; COMPND 5 SYNONYM: DEMETHYLASE,DMTASE,METHYL-CPG-BINDING PROTEIN MBD2; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*TP*TP*GP*GP*C)-3'); COMPND 9 CHAIN: D, C, E, F; COMPND 10 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: MBD2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-V2R-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28-MHL; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS DNA METHYLATION, DNA BINDING, STRUCTURAL GENOMICS, STRUCTURAL KEYWDS 2 GENOMICS CONSORTIUM, SGC, TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.LIU,C.XU,J.MIN,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 4 04-OCT-23 6CNQ 1 REMARK REVDAT 3 23-MAY-18 6CNQ 1 JRNL REVDAT 2 18-APR-18 6CNQ 1 JRNL REVDAT 1 28-MAR-18 6CNQ 0 SPRSDE 28-MAR-18 6CNQ 6C2E JRNL AUTH K.LIU,C.XU,M.LEI,A.YANG,P.LOPPNAU,T.R.HUGHES,J.MIN JRNL TITL STRUCTURAL BASIS FOR THE ABILITY OF MBD DOMAINS TO BIND JRNL TITL 2 METHYL-CG AND TG SITES IN DNA. JRNL REF J. BIOL. CHEM. V. 293 7344 2018 JRNL REFN ESSN 1083-351X JRNL PMID 29567833 JRNL DOI 10.1074/JBC.RA118.001785 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 40238 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) : 0.206 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.470 REMARK 3 FREE R VALUE TEST SET COUNT : 1398 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 24.3457 - 4.6242 0.98 3836 134 0.1352 0.1300 REMARK 3 2 4.6242 - 3.6745 1.00 3843 140 0.1620 0.1540 REMARK 3 3 3.6745 - 3.2112 0.98 3934 84 0.2073 0.2943 REMARK 3 4 3.2112 - 2.9181 1.00 3833 140 0.2752 0.3202 REMARK 3 5 2.9181 - 2.7092 1.00 3830 196 0.3030 0.3946 REMARK 3 6 2.7092 - 2.5497 1.00 3848 200 0.2859 0.3348 REMARK 3 7 2.5497 - 2.4221 1.00 4078 0 0.2870 0.0000 REMARK 3 8 2.4221 - 2.3168 1.00 3860 232 0.2945 0.2841 REMARK 3 9 2.3168 - 2.2276 1.00 4028 0 0.3134 0.0000 REMARK 3 10 2.2276 - 2.1508 1.00 3750 272 0.3294 0.3280 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.03 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 : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 34.7570 20.5638 -4.7351 REMARK 3 T TENSOR REMARK 3 T11: 0.8684 T22: 0.5676 REMARK 3 T33: 0.4478 T12: 0.0297 REMARK 3 T13: -0.0182 T23: 0.0512 REMARK 3 L TENSOR REMARK 3 L11: 0.5451 L22: 1.0680 REMARK 3 L33: 1.9503 L12: 0.4996 REMARK 3 L13: 0.5891 L23: 0.7324 REMARK 3 S TENSOR REMARK 3 S11: 0.1123 S12: -0.0709 S13: -0.2480 REMARK 3 S21: -0.0234 S22: 0.0610 S23: 0.2826 REMARK 3 S31: 0.4679 S32: -0.8633 S33: -0.0119 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): 28.3925 10.4090 -30.4128 REMARK 3 T TENSOR REMARK 3 T11: 0.7372 T22: 0.7926 REMARK 3 T33: 0.5757 T12: 0.0614 REMARK 3 T13: -0.0394 T23: 0.0328 REMARK 3 L TENSOR REMARK 3 L11: 1.0141 L22: 0.7528 REMARK 3 L33: 2.5816 L12: 0.4945 REMARK 3 L13: 0.6668 L23: 0.9721 REMARK 3 S TENSOR REMARK 3 S11: 0.1626 S12: -0.2655 S13: -0.6375 REMARK 3 S21: 0.4777 S22: -0.3303 S23: 0.2312 REMARK 3 S31: 0.6695 S32: -1.0871 S33: -0.0734 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN C REMARK 3 ORIGIN FOR THE GROUP (A): 48.6688 26.0576 1.0116 REMARK 3 T TENSOR REMARK 3 T11: 0.9753 T22: 0.5301 REMARK 3 T33: 0.6421 T12: 0.0594 REMARK 3 T13: -0.0093 T23: 0.0629 REMARK 3 L TENSOR REMARK 3 L11: 1.0429 L22: 0.1031 REMARK 3 L33: 0.7303 L12: -0.2702 REMARK 3 L13: 0.5893 L23: 0.0108 REMARK 3 S TENSOR REMARK 3 S11: 0.3373 S12: 0.5493 S13: 0.2508 REMARK 3 S21: -0.1771 S22: -0.6659 S23: -0.6312 REMARK 3 S31: 0.1579 S32: 0.3782 S33: -0.0035 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): 48.4784 26.0799 1.8980 REMARK 3 T TENSOR REMARK 3 T11: 0.9752 T22: 0.5872 REMARK 3 T33: 0.6609 T12: 0.0591 REMARK 3 T13: -0.0711 T23: 0.0285 REMARK 3 L TENSOR REMARK 3 L11: 0.2450 L22: 0.2651 REMARK 3 L33: 0.5506 L12: 0.2302 REMARK 3 L13: -0.1892 L23: -0.0785 REMARK 3 S TENSOR REMARK 3 S11: -0.2861 S12: 0.3057 S13: 0.1518 REMARK 3 S21: 1.1158 S22: -0.1247 S23: -0.5344 REMARK 3 S31: -0.0796 S32: 0.2199 S33: -0.0068 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN E REMARK 3 ORIGIN FOR THE GROUP (A): 39.5728 19.7541 -37.5497 REMARK 3 T TENSOR REMARK 3 T11: 0.7361 T22: 0.6429 REMARK 3 T33: 0.7326 T12: 0.5868 REMARK 3 T13: -0.0155 T23: 0.0197 REMARK 3 L TENSOR REMARK 3 L11: 0.8462 L22: 1.5871 REMARK 3 L33: 0.9464 L12: 0.8819 REMARK 3 L13: 0.3914 L23: -0.0639 REMARK 3 S TENSOR REMARK 3 S11: 0.9654 S12: 0.8709 S13: 0.5999 REMARK 3 S21: -0.2882 S22: -1.4686 S23: -0.4951 REMARK 3 S31: -0.2076 S32: 0.1737 S33: -0.8965 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN F REMARK 3 ORIGIN FOR THE GROUP (A): 39.7080 20.2761 -35.9768 REMARK 3 T TENSOR REMARK 3 T11: 0.7019 T22: 0.5147 REMARK 3 T33: 0.6257 T12: 0.3280 REMARK 3 T13: -0.1287 T23: 0.0186 REMARK 3 L TENSOR REMARK 3 L11: 0.9480 L22: 0.2658 REMARK 3 L33: 1.5297 L12: 0.5077 REMARK 3 L13: 0.0503 L23: -0.2847 REMARK 3 S TENSOR REMARK 3 S11: -0.4870 S12: -0.0144 S13: 0.1605 REMARK 3 S21: 1.0587 S22: 0.1951 S23: -0.4810 REMARK 3 S31: -0.1932 S32: -0.0521 S33: -0.3645 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ARP/WARP WAS USED IN MAP IMPROVEMENT REMARK 3 MODE. REFMAC WAS USED AT INTERMEDIATE STAGES OF REFINEMENT. COOT REMARK 3 WAS USED FOR INTERACTIVE MODEL BUILDING. MODEL GEOMETRY WAS REMARK 3 ASSESSED ON THE MOLPROBITY SERVER. REMARK 4 REMARK 4 6CNQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1000233102. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20266 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 40.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.86400 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: EARLIER VERSION OF PDB ENTRY 6C2K, UNPUBLISHED DNA REMARK 200 MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG-3350, 0.2M AMMONIUM FORMATE, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.63200 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 135.26400 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 3800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, 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 350 REMARK 350 BIOMOLECULE: 2 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: 3840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, E, F 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 142 REMARK 465 ALA A 143 REMARK 465 THR A 144 REMARK 465 GLU A 145 REMARK 465 SER A 146 REMARK 465 GLY A 147 REMARK 465 SER A 216 REMARK 465 LYS A 217 REMARK 465 LEU A 218 REMARK 465 GLN A 219 REMARK 465 LYS A 220 REMARK 465 GLY B 142 REMARK 465 ALA B 143 REMARK 465 THR B 144 REMARK 465 GLU B 145 REMARK 465 SER B 146 REMARK 465 GLY B 147 REMARK 465 SER B 216 REMARK 465 LYS B 217 REMARK 465 LEU B 218 REMARK 465 GLN B 219 REMARK 465 LYS B 220 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 148 CG CD CE NZ REMARK 470 LYS A 160 NZ REMARK 470 LYS A 161 NZ REMARK 470 LYS A 174 CD CE NZ REMARK 470 LYS A 185 CD CE NZ REMARK 470 ARG A 195 CD NE CZ NH1 NH2 REMARK 470 SER A 205 OG REMARK 470 LYS A 212 CG CD CE NZ REMARK 470 MET A 214 SD CE REMARK 470 LYS B 148 CG CD CE NZ REMARK 470 MET B 150 CG SD CE REMARK 470 LYS B 160 CE NZ REMARK 470 LYS B 161 NZ REMARK 470 LYS B 167 CE NZ REMARK 470 LYS B 174 CD CE NZ 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 DC E 12 UNK UNX E 102 1.30 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 D 10 O3' DG D 10 C3' -0.043 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 DC F 3 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 6CNQ A 143 220 UNP Q9UBB5 MBD2_HUMAN 143 220 DBREF 6CNQ B 143 220 UNP Q9UBB5 MBD2_HUMAN 143 220 DBREF 6CNQ D 1 12 PDB 6CNQ 6CNQ 1 12 DBREF 6CNQ C 1 12 PDB 6CNQ 6CNQ 1 12 DBREF 6CNQ E 1 12 PDB 6CNQ 6CNQ 1 12 DBREF 6CNQ F 1 12 PDB 6CNQ 6CNQ 1 12 SEQADV 6CNQ GLY A 142 UNP Q9UBB5 EXPRESSION TAG SEQADV 6CNQ GLY B 142 UNP Q9UBB5 EXPRESSION TAG SEQRES 1 A 79 GLY ALA THR GLU SER GLY LYS ARG MET ASP CYS PRO ALA SEQRES 2 A 79 LEU PRO PRO GLY TRP LYS LYS GLU GLU VAL ILE ARG LYS SEQRES 3 A 79 SER GLY LEU SER ALA GLY LYS SER ASP VAL TYR TYR PHE SEQRES 4 A 79 SER PRO SER GLY LYS LYS PHE ARG SER LYS PRO GLN LEU SEQRES 5 A 79 ALA ARG TYR LEU GLY ASN THR VAL ASP LEU SER SER PHE SEQRES 6 A 79 ASP PHE ARG THR GLY LYS MET MET PRO SER LYS LEU GLN SEQRES 7 A 79 LYS SEQRES 1 B 79 GLY ALA THR GLU SER GLY LYS ARG MET ASP CYS PRO ALA SEQRES 2 B 79 LEU PRO PRO GLY TRP LYS LYS GLU GLU VAL ILE ARG LYS SEQRES 3 B 79 SER GLY LEU SER ALA GLY LYS SER ASP VAL TYR TYR PHE SEQRES 4 B 79 SER PRO SER GLY LYS LYS PHE ARG SER LYS PRO GLN LEU SEQRES 5 B 79 ALA ARG TYR LEU GLY ASN THR VAL ASP LEU SER SER PHE SEQRES 6 B 79 ASP PHE ARG THR GLY LYS MET MET PRO SER LYS LEU GLN SEQRES 7 B 79 LYS SEQRES 1 D 12 DG DC DC DA DA 5CM DG DT DT DG DG DC SEQRES 1 C 12 DG DC DC DA DA 5CM DG DT DT DG DG DC SEQRES 1 E 12 DG DC DC DA DA 5CM DG DT DT DG DG DC SEQRES 1 F 12 DG DC DC DA DA 5CM DG DT DT DG DG DC HET 5CM D 6 27 HET 5CM C 6 20 HET 5CM E 6 20 HET 5CM F 6 20 HET UNX B 301 1 HET UNX E 101 1 HET UNX E 102 1 HET UNX F 101 1 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM UNX UNKNOWN ATOM OR ION FORMUL 3 5CM 4(C10 H16 N3 O7 P) FORMUL 7 UNX 4(X) FORMUL 11 HOH *29(H2 O) HELIX 1 AA1 SER A 189 GLY A 198 1 10 HELIX 2 AA2 ASN A 199 VAL A 201 5 3 HELIX 3 AA3 SER B 189 GLY B 198 1 10 HELIX 4 AA4 ASN B 199 VAL B 201 5 3 SHEET 1 AA1 4 MET A 150 ASP A 151 0 SHEET 2 AA1 4 LYS A 160 ILE A 165 -1 O LYS A 161 N MET A 150 SHEET 3 AA1 4 SER A 175 PHE A 180 -1 O PHE A 180 N LYS A 160 SHEET 4 AA1 4 LYS A 186 PHE A 187 -1 O PHE A 187 N TYR A 179 SHEET 1 AA2 2 PHE A 206 ASP A 207 0 SHEET 2 AA2 2 LYS A 212 MET A 213 -1 O LYS A 212 N ASP A 207 SHEET 1 AA3 4 MET B 150 ASP B 151 0 SHEET 2 AA3 4 LYS B 160 ILE B 165 -1 O LYS B 161 N MET B 150 SHEET 3 AA3 4 SER B 175 PHE B 180 -1 O TYR B 178 N GLU B 162 SHEET 4 AA3 4 LYS B 186 PHE B 187 -1 O PHE B 187 N TYR B 179 SHEET 1 AA4 2 PHE B 206 ASP B 207 0 SHEET 2 AA4 2 LYS B 212 MET B 213 -1 O LYS B 212 N ASP B 207 LINK O3' DA D 5 P 5CM D 6 1555 1555 1.60 LINK O3'A5CM D 6 P A DG D 7 1555 1555 1.61 LINK O3'B5CM D 6 P B DG D 7 1555 1555 1.61 LINK O3' DA C 5 P 5CM C 6 1555 1555 1.60 LINK O3' 5CM C 6 P DG C 7 1555 1555 1.60 LINK O3' DA E 5 P 5CM E 6 1555 1555 1.60 LINK O3' 5CM E 6 P DG E 7 1555 1555 1.60 LINK O3' DA F 5 P 5CM F 6 1555 1555 1.60 LINK O3' 5CM F 6 P DG F 7 1555 1555 1.61 CRYST1 40.500 40.500 202.896 90.00 90.00 120.00 P 31 12 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 0.024691 0.014256 0.000000 0.00000 SCALE2 0.000000 0.028511 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004929 0.00000