HEADER TRANSCRIPTION/DNA 12-FEB-18 6CEV TITLE MBD3 MBD IN COMPLEX WITH METHYLATED, NON-PALINDROMIC CPG DNA: TITLE 2 ALTERNATIVE INTERPRETATION OF CRYSTALLOGRAPHIC DATA COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYL-CPG-BINDING DOMAIN PROTEIN 3; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 1-71; COMPND 5 SYNONYM: METHYL-CPG-BINDING PROTEIN MBD3; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*GP*CP*CP*AP*GP*(5CM)P*GP*TP*TP*GP*GP*C)-3'); COMPND 9 CHAIN: C, E; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*CP*TP*GP*GP*C)-3'); COMPND 13 CHAIN: D, F; COMPND 14 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: MBD3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-V2R-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28-GSTLIC; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 17 ORGANISM_TAXID: 32630 KEYWDS STRUCTURAL GENOMICS CONSORTIUM, SGC, TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.LIU,W.TEMPEL,A.K.WERNIMONT,C.BOUNTRA,C.H.ARROWSMITH,A.M.EDWARDS, AUTHOR 2 J.MIN,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 4 04-OCT-23 6CEV 1 REMARK REVDAT 3 04-SEP-19 6CEV 1 JRNL REVDAT 2 22-MAY-19 6CEV 1 JRNL REVDAT 1 09-MAY-18 6CEV 0 JRNL AUTH K.LIU,M.LEI,Z.WU,B.GAN,H.CHENG,Y.LI,J.MIN JRNL TITL STRUCTURAL ANALYSES REVEAL THAT MBD3 IS A METHYLATED CG JRNL TITL 2 BINDER. JRNL REF FEBS J. V. 286 3240 2019 JRNL REFN ISSN 1742-464X JRNL PMID 30980593 JRNL DOI 10.1111/FEBS.14850 REMARK 2 REMARK 2 RESOLUTION. 2.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 22928 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.720 REMARK 3 FREE R VALUE TEST SET COUNT : 1312 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 35.2069 - 4.1692 0.99 2517 144 0.1734 0.2201 REMARK 3 2 4.1692 - 3.3100 0.98 2364 140 0.1855 0.2190 REMARK 3 3 3.3100 - 2.8918 0.99 2384 162 0.2389 0.2862 REMARK 3 4 2.8918 - 2.6275 1.00 2429 152 0.2710 0.2894 REMARK 3 5 2.6275 - 2.4392 1.00 2413 134 0.2599 0.2909 REMARK 3 6 2.4392 - 2.2954 1.00 2458 113 0.2480 0.3155 REMARK 3 7 2.2954 - 2.1805 1.00 2400 132 0.2575 0.3117 REMARK 3 8 2.1805 - 2.0856 1.00 2357 182 0.2694 0.3167 REMARK 3 9 2.0856 - 2.0053 0.99 2294 153 0.2735 0.3203 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.95 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.33 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 : 0.007 2224 REMARK 3 ANGLE : 1.103 3203 REMARK 3 CHIRALITY : 0.065 330 REMARK 3 PLANARITY : 0.008 247 REMARK 3 DIHEDRAL : 26.794 1142 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): -23.7768 -4.5334 55.2488 REMARK 3 T TENSOR REMARK 3 T11: 0.4067 T22: 0.3157 REMARK 3 T33: 0.2738 T12: 0.0421 REMARK 3 T13: -0.0267 T23: -0.0188 REMARK 3 L TENSOR REMARK 3 L11: 2.9346 L22: 3.5642 REMARK 3 L33: 8.4591 L12: 0.3002 REMARK 3 L13: 0.3657 L23: -3.9393 REMARK 3 S TENSOR REMARK 3 S11: 0.1227 S12: -0.1599 S13: -0.0986 REMARK 3 S21: 0.0461 S22: -0.0028 S23: 0.0537 REMARK 3 S31: 0.2486 S32: -0.2835 S33: -0.1338 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): -20.7916 6.5201 10.1366 REMARK 3 T TENSOR REMARK 3 T11: 0.4121 T22: 0.2793 REMARK 3 T33: 0.2215 T12: -0.0284 REMARK 3 T13: 0.0194 T23: -0.0162 REMARK 3 L TENSOR REMARK 3 L11: 3.4261 L22: 3.4059 REMARK 3 L33: 6.2837 L12: -0.5907 REMARK 3 L13: -0.8021 L23: -3.8210 REMARK 3 S TENSOR REMARK 3 S11: 0.1229 S12: 0.2515 S13: 0.0746 REMARK 3 S21: -0.0564 S22: -0.0384 S23: 0.0355 REMARK 3 S31: -0.2036 S32: -0.3618 S33: -0.0722 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN C REMARK 3 ORIGIN FOR THE GROUP (A): -19.6240 7.7646 45.0306 REMARK 3 T TENSOR REMARK 3 T11: 0.3318 T22: 0.4642 REMARK 3 T33: 0.4115 T12: 0.1478 REMARK 3 T13: 0.0480 T23: -0.0169 REMARK 3 L TENSOR REMARK 3 L11: 1.1074 L22: 1.5369 REMARK 3 L33: 2.0650 L12: 0.4346 REMARK 3 L13: -0.6103 L23: 1.2951 REMARK 3 S TENSOR REMARK 3 S11: 0.1810 S12: 0.5830 S13: 0.2214 REMARK 3 S21: 0.0211 S22: -0.1174 S23: 0.0058 REMARK 3 S31: -0.1480 S32: 0.3085 S33: -0.0859 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): -19.4150 8.2890 46.2915 REMARK 3 T TENSOR REMARK 3 T11: 0.2778 T22: 0.3385 REMARK 3 T33: 0.3454 T12: 0.0425 REMARK 3 T13: 0.0024 T23: -0.0174 REMARK 3 L TENSOR REMARK 3 L11: 6.2530 L22: 4.8164 REMARK 3 L33: 2.2891 L12: -4.2103 REMARK 3 L13: 1.1398 L23: -0.0859 REMARK 3 S TENSOR REMARK 3 S11: -0.1942 S12: 0.1685 S13: 0.1363 REMARK 3 S21: -0.0061 S22: -0.0307 S23: -0.0715 REMARK 3 S31: -0.1926 S32: 0.1022 S33: 0.2444 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN E REMARK 3 ORIGIN FOR THE GROUP (A): -16.5615 -5.6901 20.4875 REMARK 3 T TENSOR REMARK 3 T11: 0.3512 T22: 0.4246 REMARK 3 T33: 0.3713 T12: -0.1092 REMARK 3 T13: -0.0363 T23: -0.0480 REMARK 3 L TENSOR REMARK 3 L11: 2.6275 L22: 2.3995 REMARK 3 L33: 1.9487 L12: 0.6555 REMARK 3 L13: 1.5952 L23: 1.0870 REMARK 3 S TENSOR REMARK 3 S11: 0.0800 S12: -0.9242 S13: 0.0607 REMARK 3 S21: -0.2124 S22: -0.1788 S23: -0.1107 REMARK 3 S31: -0.2280 S32: 0.5399 S33: 0.0987 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN F REMARK 3 ORIGIN FOR THE GROUP (A): -16.3427 -6.2564 19.1924 REMARK 3 T TENSOR REMARK 3 T11: 0.3242 T22: 0.2588 REMARK 3 T33: 0.3877 T12: -0.0055 REMARK 3 T13: -0.0371 T23: -0.0001 REMARK 3 L TENSOR REMARK 3 L11: 5.9243 L22: 3.1866 REMARK 3 L33: 3.1153 L12: 3.0589 REMARK 3 L13: -1.6426 L23: 0.0987 REMARK 3 S TENSOR REMARK 3 S11: -0.1273 S12: -0.4337 S13: -0.2029 REMARK 3 S21: -0.0289 S22: -0.0506 S23: -0.1509 REMARK 3 S31: 0.1459 S32: 0.1414 S33: 0.1853 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ELECTRON DENSITY DID NOT PERMIT REMARK 3 UNAMBIGUOUS DISTINCTION BETWEEN STRANDS OF NON-PALINDROMIC DNA. REMARK 3 REFMAC WAS USED FOR INTERMEDIATE REFINEMENT STEPS. COOT WAS USED REMARK 3 FOR INTERACTIVE MODEL BUILDING. MODEL GEOMETRY WAS VALIDATED REMARK 3 WITH MOLPROBITY. REMARK 4 REMARK 4 6CEV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1000232624. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97911 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 0.5.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23289 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 43.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1000 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) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.82600 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: EARLY VERSION OF MODEL FROM PDB ENTRY 6CC8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3350, 0.2M SODIUM CHLORIDE, REMARK 280 0.1M BIS-TRIS, PH 6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 36.08700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.11150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 36.08700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.11150 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 3790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 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 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: 3760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 -1 REMARK 465 SER A 0 REMARK 465 GLY B -1 REMARK 465 SER B 0 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 MET A 1 CG SD CE REMARK 470 GLU A 2 CG CD OE1 OE2 REMARK 470 LYS A 4 CD CE NZ REMARK 470 GLU A 7 CG CD OE1 OE2 REMARK 470 GLN A 13 CG CD OE1 NE2 REMARK 470 ARG A 23 CD NE CZ NH1 NH2 REMARK 470 LEU A 26 CD1 CD2 REMARK 470 SER A 56 OG REMARK 470 ARG A 65 NE CZ NH1 NH2 REMARK 470 MET A 71 CG SD CE REMARK 470 MET B 1 CG SD CE REMARK 470 GLU B 2 CG CD OE1 OE2 REMARK 470 ARG B 3 NE CZ NH1 NH2 REMARK 470 GLU B 7 CG CD OE1 OE2 REMARK 470 ARG B 23 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 65 NE CZ NH1 NH2 REMARK 470 LYS B 68 CE NZ REMARK 470 MET B 71 CA C O CB CG SD CE 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 DA C 4 O4' - C1' - N9 ANGL. DEV. = -4.5 DEGREES REMARK 500 DT D 9 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC E 3 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC E 12 O4' - C1' - N1 ANGL. DEV. = 1.9 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 TRP A 6 -166.71 -169.80 REMARK 500 TRP B 6 -167.57 -169.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6CEU RELATED DB: PDB REMARK 900 ALTERNATIVE ASSIGNMENT OF DNA STRANDS DBREF 6CEV A 1 71 UNP O95983 MBD3_HUMAN 1 71 DBREF 6CEV B 1 71 UNP O95983 MBD3_HUMAN 1 71 DBREF 6CEV C 1 12 PDB 6CEV 6CEV 1 12 DBREF 6CEV D 1 12 PDB 6CEV 6CEV 1 12 DBREF 6CEV E 1 12 PDB 6CEV 6CEV 1 12 DBREF 6CEV F 1 12 PDB 6CEV 6CEV 1 12 SEQADV 6CEV GLY A -1 UNP O95983 EXPRESSION TAG SEQADV 6CEV SER A 0 UNP O95983 EXPRESSION TAG SEQADV 6CEV GLY B -1 UNP O95983 EXPRESSION TAG SEQADV 6CEV SER B 0 UNP O95983 EXPRESSION TAG SEQRES 1 A 73 GLY SER MET GLU ARG LYS ARG TRP GLU CYS PRO ALA LEU SEQRES 2 A 73 PRO GLN GLY TRP GLU ARG GLU GLU VAL PRO ARG ARG SER SEQRES 3 A 73 GLY LEU SER ALA GLY HIS ARG ASP VAL PHE TYR TYR SER SEQRES 4 A 73 PRO SER GLY LYS LYS PHE ARG SER LYS PRO GLN LEU ALA SEQRES 5 A 73 ARG TYR LEU GLY GLY SER MET ASP LEU SER THR PHE ASP SEQRES 6 A 73 PHE ARG THR GLY LYS MET LEU MET SEQRES 1 B 73 GLY SER MET GLU ARG LYS ARG TRP GLU CYS PRO ALA LEU SEQRES 2 B 73 PRO GLN GLY TRP GLU ARG GLU GLU VAL PRO ARG ARG SER SEQRES 3 B 73 GLY LEU SER ALA GLY HIS ARG ASP VAL PHE TYR TYR SER SEQRES 4 B 73 PRO SER GLY LYS LYS PHE ARG SER LYS PRO GLN LEU ALA SEQRES 5 B 73 ARG TYR LEU GLY GLY SER MET ASP LEU SER THR PHE ASP SEQRES 6 B 73 PHE ARG THR GLY LYS MET LEU MET SEQRES 1 C 12 DG DC DC DA DG 5CM DG DT DT DG DG DC SEQRES 1 D 12 DG DC DC DA DA 5CM DG DC DT DG DG DC SEQRES 1 E 12 DG DC DC DA DG 5CM DG DT DT DG DG DC SEQRES 1 F 12 DG DC DC DA DA 5CM DG DC DT DG DG DC HET 5CM C 6 20 HET 5CM D 6 20 HET 5CM E 6 20 HET 5CM F 6 20 HET UNX A 101 1 HET UNX C 101 1 HET UNX F 101 1 HET UNX F 102 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 *66(H2 O) HELIX 1 AA1 SER A 45 GLY A 54 1 10 HELIX 2 AA2 SER B 45 GLY B 54 1 10 SHEET 1 AA1 4 LYS A 4 GLU A 7 0 SHEET 2 AA1 4 GLU A 16 PRO A 21 -1 O ARG A 17 N TRP A 6 SHEET 3 AA1 4 ARG A 31 TYR A 36 -1 O ASP A 32 N VAL A 20 SHEET 4 AA1 4 LYS A 42 PHE A 43 -1 O PHE A 43 N TYR A 35 SHEET 1 AA2 2 PHE A 62 ASP A 63 0 SHEET 2 AA2 2 LYS A 68 MET A 69 -1 O LYS A 68 N ASP A 63 SHEET 1 AA3 4 LYS B 4 GLU B 7 0 SHEET 2 AA3 4 GLU B 16 PRO B 21 -1 O ARG B 17 N TRP B 6 SHEET 3 AA3 4 ARG B 31 TYR B 36 -1 O PHE B 34 N GLU B 18 SHEET 4 AA3 4 LYS B 42 PHE B 43 -1 O PHE B 43 N TYR B 35 SHEET 1 AA4 2 PHE B 62 ASP B 63 0 SHEET 2 AA4 2 LYS B 68 MET B 69 -1 O LYS B 68 N ASP B 63 LINK O3'B DG C 5 P B5CM C 6 1555 1555 1.60 LINK O3'B5CM C 6 P B DG C 7 1555 1555 1.60 LINK O3'B DA D 5 P B5CM D 6 1555 1555 1.61 LINK O3'B5CM D 6 P B DG D 7 1555 1555 1.61 LINK O3'B DG E 5 P B5CM E 6 1555 1555 1.60 LINK O3'B5CM E 6 P B DG E 7 1555 1555 1.60 LINK O3'B DA F 5 P B5CM F 6 1555 1555 1.61 LINK O3'B5CM F 6 P B DG F 7 1555 1555 1.61 CRYST1 72.174 36.223 131.157 90.00 92.85 90.00 C 1 2 1 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 0.013855 0.000000 0.000690 0.00000 SCALE2 0.000000 0.027607 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007634 0.00000