HEADER HYDROLASE/DNA 21-SEP-12 3VXV TITLE CRYSTAL STRUCTURE OF METHYL CPG BINDING DOMAIN OF MBD4 IN COMPLEX WITH TITLE 2 THE 5MCG/TG SEQUENCE COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYL-CPG-BINDING DOMAIN PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: METHYL CPG BINDING DOMAIN, UNP RESIDUES 69-136; COMPND 5 SYNONYM: METHYL-CPG-BINDING PROTEIN MBD4, MISMATCH-SPECIFIC DNA N- COMPND 6 GLYCOSYLASE; COMPND 7 EC: 3.2.2.-; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(*GP*TP*CP*AP*CP*TP*AP*CP*(5CM)P*GP*GP*AP*CP*A)- COMPND 11 3'); COMPND 12 CHAIN: B; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: DNA (5'-D(*GP*TP*CP*TP*GP*GP*TP*AP*GP*TP*GP*AP*CP*T)-3'); COMPND 16 CHAIN: C; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: MBD4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES KEYWDS METHYL CPG BINDING DOMAIN, PROTEIN-DNA COMPLEX, VERSATILE BASE KEYWDS 2 RECOGNITION, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.OTANI,K.ARITA,T.KATO,M.KINOSHITA,M.ARIYOSHI,M.SHIRAKAWA REVDAT 2 14-AUG-13 3VXV 1 JRNL REVDAT 1 16-JAN-13 3VXV 0 JRNL AUTH J.OTANI,K.ARITA,T.KATO,M.KINOSHITA,H.KIMURA,I.SUETAKE, JRNL AUTH 2 S.TAJIMA,M.ARIYOSHI,M.SHIRAKAWA JRNL TITL STRUCTURAL BASIS OF THE VERSATILE DNA RECOGNITION ABILITY OF JRNL TITL 2 THE METHYL-CPG BINDING DOMAIN OF METHYL-CPG BINDING DOMAIN JRNL TITL 3 PROTEIN 4 JRNL REF J.BIOL.CHEM. V. 288 6351 2013 JRNL REFN ISSN 0021-9258 JRNL PMID 23316048 JRNL DOI 10.1074/JBC.M112.431098 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 16002 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 801 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 23.7489 - 3.6286 0.98 2622 122 0.1626 0.1633 REMARK 3 2 3.6286 - 2.8817 1.00 2566 117 0.1711 0.2235 REMARK 3 3 2.8817 - 2.5179 1.00 2545 125 0.2178 0.2713 REMARK 3 4 2.5179 - 2.2879 1.00 2500 148 0.2338 0.2924 REMARK 3 5 2.2879 - 2.1240 0.99 2493 139 0.2553 0.3677 REMARK 3 6 2.1240 - 1.9989 1.00 2475 150 0.2332 0.2707 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.34 REMARK 3 B_SOL : 54.25 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.620 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.36 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -12.95280 REMARK 3 B22 (A**2) : 10.76750 REMARK 3 B33 (A**2) : 2.18530 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : -0.00000 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 : 0.018 1205 REMARK 3 ANGLE : 2.071 1728 REMARK 3 CHIRALITY : 0.119 185 REMARK 3 PLANARITY : 0.010 123 REMARK 3 DIHEDRAL : 23.326 479 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: chain A REMARK 3 ORIGIN FOR THE GROUP (A): -3.3944 -11.8131 4.3750 REMARK 3 T TENSOR REMARK 3 T11: 0.2326 T22: 0.2517 REMARK 3 T33: 0.2424 T12: -0.0073 REMARK 3 T13: 0.0026 T23: -0.0245 REMARK 3 L TENSOR REMARK 3 L11: 0.6284 L22: 0.9797 REMARK 3 L33: 1.5410 L12: -0.4314 REMARK 3 L13: 0.3256 L23: -0.6242 REMARK 3 S TENSOR REMARK 3 S11: 0.0083 S12: -0.0141 S13: 0.0059 REMARK 3 S21: -0.0971 S22: 0.0234 S23: -0.0729 REMARK 3 S31: 0.0997 S32: -0.0137 S33: -0.0487 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: chain B REMARK 3 ORIGIN FOR THE GROUP (A): -18.9331 -12.0063 -13.7962 REMARK 3 T TENSOR REMARK 3 T11: 0.3457 T22: 0.3937 REMARK 3 T33: 0.3550 T12: -0.0759 REMARK 3 T13: -0.0226 T23: -0.1141 REMARK 3 L TENSOR REMARK 3 L11: 1.7749 L22: 2.1899 REMARK 3 L33: 0.5161 L12: 1.6014 REMARK 3 L13: -0.4628 L23: -1.0130 REMARK 3 S TENSOR REMARK 3 S11: -0.0418 S12: -0.2728 S13: 0.2781 REMARK 3 S21: -0.2738 S22: -0.0546 S23: 0.3679 REMARK 3 S31: 0.1146 S32: 0.2262 S33: 0.0383 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: chain C REMARK 3 ORIGIN FOR THE GROUP (A): -22.6605 -13.3668 -11.2981 REMARK 3 T TENSOR REMARK 3 T11: 0.3022 T22: 0.4634 REMARK 3 T33: 0.3583 T12: -0.0426 REMARK 3 T13: -0.0095 T23: -0.0021 REMARK 3 L TENSOR REMARK 3 L11: 3.7803 L22: 0.6264 REMARK 3 L33: 0.3422 L12: 0.2987 REMARK 3 L13: 0.0373 L23: 0.3534 REMARK 3 S TENSOR REMARK 3 S11: -0.2650 S12: 0.0063 S13: -0.3741 REMARK 3 S21: -0.1841 S22: 0.1125 S23: 0.1463 REMARK 3 S31: 0.0021 S32: -0.1157 S33: 0.1730 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 3VXV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-OCT-12. REMARK 100 THE RCSB ID CODE IS RCSB095636. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JAN-10; 14-OCT-09 REMARK 200 TEMPERATURE (KELVIN) : 95; 95 REMARK 200 PH : 4.4; 4.4 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY; PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A; AR-NE3A REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000; NULL REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R; ADSC QUANTUM REMARK 200 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16062 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.03100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.36500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.4, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K. PH 4.4, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 27.36900 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 27.36900 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 44.53700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.49450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 44.53700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.49450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 27.36900 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 44.53700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.49450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 27.36900 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 44.53700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 47.49450 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL 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 320 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 201 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 SER A 68 REMARK 465 GLY A 69 REMARK 465 HIS A 70 REMARK 465 GLY A 136 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 71 CG 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 DA B 4 O HOH B 237 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 B 11 O3' DG B 11 C3' -0.051 REMARK 500 DA B 14 C6 DA B 14 N1 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 ARG A 79 NE - CZ - NH1 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG A 79 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG B 1 O4' - C1' - C2' ANGL. DEV. = 5.8 DEGREES REMARK 500 DG B 1 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC B 5 N3 - C2 - O2 ANGL. DEV. = 4.3 DEGREES REMARK 500 DT B 6 C4 - C5 - C7 ANGL. DEV. = 5.7 DEGREES REMARK 500 DT B 6 C6 - C5 - C7 ANGL. DEV. = -5.2 DEGREES REMARK 500 DC B 8 O4' - C1' - N1 ANGL. DEV. = -4.7 DEGREES REMARK 500 DG B 11 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 DA B 14 OP1 - P - OP2 ANGL. DEV. = 9.8 DEGREES REMARK 500 DA B 14 O4' - C4' - C3' ANGL. DEV. = -2.9 DEGREES REMARK 500 DA B 14 C3' - C2' - C1' ANGL. DEV. = -5.5 DEGREES REMARK 500 DA B 14 O4' - C1' - C2' ANGL. DEV. = 3.3 DEGREES REMARK 500 DG C 1 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DT C 2 C2 - N3 - C4 ANGL. DEV. = -3.7 DEGREES REMARK 500 DT C 2 C5 - C6 - N1 ANGL. DEV. = -3.6 DEGREES REMARK 500 DC C 3 C2 - N3 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 DC C 3 C5 - C6 - N1 ANGL. DEV. = -3.1 DEGREES REMARK 500 DT C 4 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES REMARK 500 DG C 5 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG C 11 C1' - O4' - C4' ANGL. DEV. = -8.4 DEGREES REMARK 500 DG C 11 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 DG C 11 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DT C 14 C5 - C4 - O4 ANGL. DEV. = -4.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO C 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VXX RELATED DB: PDB REMARK 900 RELATED ID: 3VYB RELATED DB: PDB REMARK 900 RELATED ID: 3VYQ RELATED DB: PDB DBREF 3VXV A 69 136 UNP Q9Z2D7 MBD4_MOUSE 69 136 DBREF 3VXV B 1 14 PDB 3VXV 3VXV 1 14 DBREF 3VXV C 1 14 PDB 3VXV 3VXV 1 14 SEQADV 3VXV SER A 68 UNP Q9Z2D7 EXPRESSION TAG SEQRES 1 A 69 SER GLY HIS LYS PRO VAL PRO CYS GLY TRP GLU ARG VAL SEQRES 2 A 69 VAL LYS GLN ARG LEU SER GLY LYS THR ALA GLY LYS PHE SEQRES 3 A 69 ASP VAL TYR PHE ILE SER PRO GLN GLY LEU LYS PHE ARG SEQRES 4 A 69 SER LYS ARG SER LEU ALA ASN TYR LEU LEU LYS ASN GLY SEQRES 5 A 69 GLU THR PHE LEU LYS PRO GLU ASP PHE ASN PHE THR VAL SEQRES 6 A 69 LEU PRO LYS GLY SEQRES 1 B 14 DG DT DC DA DC DT DA DC 5CM DG DG DA DC SEQRES 2 B 14 DA SEQRES 1 C 14 DG DT DC DT DG DG DT DA DG DT DG DA DC SEQRES 2 C 14 DT MODRES 3VXV 5CM B 9 DC HET 5CM B 9 20 HET ACT A 201 4 HET ACT A 202 4 HET EDO A 203 4 HET EDO A 204 4 HET EDO A 205 4 HET EDO A 206 4 HET EDO A 207 4 HET ACT B 101 4 HET EDO C 101 4 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM ACT ACETATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 5CM C10 H16 N3 O7 P FORMUL 4 ACT 3(C2 H3 O2 1-) FORMUL 6 EDO 6(C2 H6 O2) FORMUL 13 HOH *154(H2 O) HELIX 1 1 SER A 107 GLY A 119 1 13 HELIX 2 2 LYS A 124 PHE A 128 5 5 SHEET 1 A 3 GLU A 78 GLN A 83 0 SHEET 2 A 3 PHE A 93 ILE A 98 -1 O TYR A 96 N VAL A 80 SHEET 3 A 3 LYS A 104 PHE A 105 -1 O PHE A 105 N PHE A 97 SSBOND 1 CYS A 75 CYS A 75 1555 3555 2.04 LINK O3' DC B 8 P 5CM B 9 1555 1555 1.60 LINK O3' 5CM B 9 P DG B 10 1555 1555 1.61 SITE 1 AC1 3 GLU A 120 DC C 13 DT C 14 SITE 1 AC2 3 GLN A 101 ASN A 118 GLU A 120 SITE 1 AC3 5 GLN A 83 ARG A 84 HOH A 318 DC C 3 SITE 2 AC3 5 DT C 4 SITE 1 AC4 5 GLY A 76 GLU A 78 ILE A 98 SER A 99 SITE 2 AC4 5 DA B 14 SITE 1 AC5 3 CYS A 75 GLY A 76 TRP A 77 SITE 1 AC6 3 LYS A 104 PHE A 105 ACT B 101 SITE 1 AC7 3 VAL A 132 LEU A 133 PRO A 134 SITE 1 AC8 4 EDO A 206 5CM B 9 DG B 10 HOH B 248 SITE 1 AC9 3 DC B 13 DT C 2 DC C 3 CRYST1 89.074 94.989 54.738 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 0.011227 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010528 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018269 0.00000