HEADER TRANSCRIPTION/DNA 12-FEB-18 6CEU 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 SYNONYM: METHYL-CPG-BINDING PROTEIN MBD3; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*GP*CP*CP*AP*GP*(5CM)P*GP*TP*TP*GP*GP*C)-3'); COMPND 8 CHAIN: C, E; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*CP*TP*GP*GP*C)-3'); COMPND 12 CHAIN: D, F; COMPND 13 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 6CEU 1 REMARK REVDAT 3 04-SEP-19 6CEU 1 JRNL REVDAT 2 22-MAY-19 6CEU 1 JRNL REVDAT 1 09-MAY-18 6CEU 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 : NULL 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 : 0.252 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 0.1736 0.2089 REMARK 3 2 4.1692 - 3.3100 0.98 2364 140 0.1853 0.2151 REMARK 3 3 3.3100 - 2.8918 0.99 2384 162 0.2389 0.2846 REMARK 3 4 2.8918 - 2.6275 1.00 2429 152 0.2712 0.2821 REMARK 3 5 2.6275 - 2.4392 1.00 2413 134 0.2580 0.2943 REMARK 3 6 2.4392 - 2.2954 1.00 2458 113 0.2473 0.3155 REMARK 3 7 2.2954 - 2.1805 1.00 2400 132 0.2549 0.3077 REMARK 3 8 2.1805 - 2.0856 1.00 2357 182 0.2692 0.3140 REMARK 3 9 2.0856 - 2.0053 0.99 2294 153 0.2718 0.3233 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.780 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.95 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.11 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 : 1.101 3203 REMARK 3 CHIRALITY : 0.064 330 REMARK 3 PLANARITY : 0.007 247 REMARK 3 DIHEDRAL : 26.814 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): -23.7783 -4.5468 55.2502 REMARK 3 T TENSOR REMARK 3 T11: 0.4053 T22: 0.3236 REMARK 3 T33: 0.2809 T12: 0.0274 REMARK 3 T13: -0.0266 T23: -0.0124 REMARK 3 L TENSOR REMARK 3 L11: 2.5548 L22: 2.8322 REMARK 3 L33: 8.2239 L12: 0.1089 REMARK 3 L13: 0.5077 L23: -3.5242 REMARK 3 S TENSOR REMARK 3 S11: 0.1246 S12: -0.1570 S13: -0.1096 REMARK 3 S21: -0.0061 S22: -0.0152 S23: 0.0485 REMARK 3 S31: 0.2101 S32: -0.2799 S33: -0.1178 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): -20.7896 6.5096 10.1363 REMARK 3 T TENSOR REMARK 3 T11: 0.4314 T22: 0.2972 REMARK 3 T33: 0.2324 T12: -0.0312 REMARK 3 T13: 0.0036 T23: -0.0171 REMARK 3 L TENSOR REMARK 3 L11: 2.9298 L22: 3.2940 REMARK 3 L33: 5.6389 L12: -0.6690 REMARK 3 L13: -1.2032 L23: -3.7531 REMARK 3 S TENSOR REMARK 3 S11: 0.1122 S12: 0.2250 S13: 0.0720 REMARK 3 S21: -0.0354 S22: -0.0751 S23: 0.0213 REMARK 3 S31: -0.2697 S32: -0.3142 S33: -0.0487 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN C REMARK 3 ORIGIN FOR THE GROUP (A): -19.4262 8.2703 46.2634 REMARK 3 T TENSOR REMARK 3 T11: 0.3196 T22: 0.3441 REMARK 3 T33: 0.3713 T12: 0.0606 REMARK 3 T13: 0.0140 T23: -0.0184 REMARK 3 L TENSOR REMARK 3 L11: 5.9913 L22: 4.4982 REMARK 3 L33: 2.3439 L12: -3.8632 REMARK 3 L13: 1.5048 L23: -0.2177 REMARK 3 S TENSOR REMARK 3 S11: -0.1110 S12: 0.1864 S13: 0.2419 REMARK 3 S21: -0.0777 S22: -0.0603 S23: -0.1566 REMARK 3 S31: -0.1647 S32: 0.1424 S33: 0.2172 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): -19.6367 7.7380 45.0069 REMARK 3 T TENSOR REMARK 3 T11: 0.2894 T22: 0.4402 REMARK 3 T33: 0.3936 T12: 0.1320 REMARK 3 T13: 0.0315 T23: -0.0228 REMARK 3 L TENSOR REMARK 3 L11: 1.0493 L22: 1.4556 REMARK 3 L33: 2.2333 L12: 0.5625 REMARK 3 L13: -0.5798 L23: 1.1775 REMARK 3 S TENSOR REMARK 3 S11: 0.1243 S12: 0.5538 S13: 0.2113 REMARK 3 S21: 0.0529 S22: -0.0865 S23: 0.0192 REMARK 3 S31: -0.1843 S32: 0.3157 S33: -0.0822 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN E REMARK 3 ORIGIN FOR THE GROUP (A): -16.3508 -6.2599 19.2217 REMARK 3 T TENSOR REMARK 3 T11: 0.3405 T22: 0.2869 REMARK 3 T33: 0.3875 T12: -0.0220 REMARK 3 T13: -0.0439 T23: -0.0112 REMARK 3 L TENSOR REMARK 3 L11: 6.3059 L22: 2.7313 REMARK 3 L33: 2.8117 L12: 3.1217 REMARK 3 L13: -1.6122 L23: 0.0098 REMARK 3 S TENSOR REMARK 3 S11: -0.0587 S12: -0.4915 S13: -0.2184 REMARK 3 S21: -0.1070 S22: -0.0524 S23: -0.1661 REMARK 3 S31: 0.0586 S32: 0.2051 S33: 0.1427 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN F REMARK 3 ORIGIN FOR THE GROUP (A): -16.5755 -5.6847 20.5195 REMARK 3 T TENSOR REMARK 3 T11: 0.3701 T22: 0.4206 REMARK 3 T33: 0.3402 T12: -0.1215 REMARK 3 T13: -0.0472 T23: -0.0540 REMARK 3 L TENSOR REMARK 3 L11: 2.1845 L22: 1.9384 REMARK 3 L33: 2.3586 L12: 0.1647 REMARK 3 L13: 0.9164 L23: 0.7142 REMARK 3 S TENSOR REMARK 3 S11: 0.0539 S12: -0.8996 S13: 0.0541 REMARK 3 S21: -0.1877 S22: -0.1958 S23: -0.0985 REMARK 3 S31: -0.2170 S32: 0.4997 S33: 0.0644 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 6CEU 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_1000232536. 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: 3840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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: 3750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7600 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 -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 DC D 3 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DA D 4 O4' - C1' - N9 ANGL. DEV. = -4.4 DEGREES REMARK 500 DC F 3 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC F 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 -167.34 -170.06 REMARK 500 TRP B 6 -167.79 -169.86 REMARK 500 REMARK 500 REMARK: NULL DBREF 6CEU A 1 71 UNP O95983 MBD3_HUMAN 1 71 DBREF 6CEU B 1 71 UNP O95983 MBD3_HUMAN 1 71 DBREF 6CEU C 1 12 PDB 6CEU 6CEU 1 12 DBREF 6CEU D 1 12 PDB 6CEU 6CEU 1 12 DBREF 6CEU E 1 12 PDB 6CEU 6CEU 1 12 DBREF 6CEU F 1 12 PDB 6CEU 6CEU 1 12 SEQADV 6CEU GLY A -1 UNP O95983 EXPRESSION TAG SEQADV 6CEU SER A 0 UNP O95983 EXPRESSION TAG SEQADV 6CEU GLY B -1 UNP O95983 EXPRESSION TAG SEQADV 6CEU 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 C 101 1 HET UNX D 101 1 HET UNX E 101 1 HET UNX E 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 TYR B 36 N GLU B 16 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'A DG C 5 P A5CM C 6 1555 1555 1.61 LINK O3'A5CM C 6 P A DG C 7 1555 1555 1.61 LINK O3'A DA D 5 P A5CM D 6 1555 1555 1.61 LINK O3'A5CM D 6 P A DG D 7 1555 1555 1.60 LINK O3'A DG E 5 P A5CM E 6 1555 1555 1.61 LINK O3'A5CM E 6 P A DG E 7 1555 1555 1.61 LINK O3'A DA F 5 P A5CM F 6 1555 1555 1.61 LINK O3'A5CM F 6 P A DG F 7 1555 1555 1.60 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