PDB Short entry for 6C1Y HEADER DNA BINDING PROTEIN/DNA 05-JAN-18 6C1Y TITLE MBD OF HUMAN MECP2 IN COMPLEX WITH METHYLATED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYL-CPG-BINDING PROTEIN 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: MECP2; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 12-MER DNA; COMPND 8 CHAIN: D, C, F, E; COMPND 9 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: MECP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-V2R-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28-MHL; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630; SOURCE 14 OTHER_DETAILS: SYNTHETIC DNA KEYWDS MBD, DNA METHYLATION, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS KEYWDS 2 CONSORTIUM, SGC, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.LIU,C.BIAN,W.TEMPEL,A.K.WERNIMONT,C.H.ARROWSMITH,C.BOUNTRA, AUTHOR 2 A.M.EDWARDS,J.MIN,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 3 04-OCT-23 6C1Y 1 REMARK REVDAT 2 20-NOV-19 6C1Y 1 JRNL REVDAT 1 14-FEB-18 6C1Y 0 JRNL AUTH M.LEI,W.TEMPEL,S.CHEN,K.LIU,J.MIN JRNL TITL PLASTICITY AT THE DNA RECOGNITION SITE OF THE MECP2 JRNL TITL 2 MCG-BINDING DOMAIN. JRNL REF BIOCHIM BIOPHYS ACTA GENE V.1862 94409 2019 JRNL REF 2 REGUL MECH JRNL REFN ISSN 1876-4320 JRNL PMID 31356990 JRNL DOI 10.1016/J.BBAGRM.2019.194409 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 13799 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.400 REMARK 3 FREE R VALUE TEST SET COUNT : 785 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 837 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.45 REMARK 3 BIN R VALUE (WORKING SET) : 0.3500 REMARK 3 BIN FREE R VALUE SET COUNT : 96 REMARK 3 BIN FREE R VALUE : 0.4430 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1090 REMARK 3 NUCLEIC ACID ATOMS : 976 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 65.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.22000 REMARK 3 B22 (A**2) : 1.74000 REMARK 3 B33 (A**2) : -2.35000 REMARK 3 B12 (A**2) : -1.93000 REMARK 3 B13 (A**2) : 1.86000 REMARK 3 B23 (A**2) : -2.26000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.335 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.262 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.257 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 25.521 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2210 ; 0.016 ; 0.016 REMARK 3 BOND LENGTHS OTHERS (A): 1534 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3196 ; 1.669 ; 1.610 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3576 ; 1.316 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 140 ; 5.819 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 49 ;30.819 ;23.878 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 171 ;15.157 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;28.612 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 303 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1824 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 474 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 566 ; 2.294 ; 5.098 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 565 ; 2.296 ; 5.098 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 704 ; 3.472 ; 7.638 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 7 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 92 162 B 92 162 4006 0.090 0.050 REMARK 3 2 D 1 12 C 1 12 2080 0.030 0.050 REMARK 3 3 D 1 12 F 1 12 2038 0.080 0.050 REMARK 3 4 D 1 12 E 1 12 2050 0.060 0.050 REMARK 3 5 C 1 12 F 1 12 2030 0.090 0.050 REMARK 3 6 C 1 12 E 1 12 2070 0.050 0.050 REMARK 3 7 F 1 12 E 1 12 2012 0.100 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 92 A 162 REMARK 3 ORIGIN FOR THE GROUP (A): -19.0698 -3.8257 -1.7757 REMARK 3 T TENSOR REMARK 3 T11: 0.1847 T22: 0.1540 REMARK 3 T33: 0.0363 T12: -0.0437 REMARK 3 T13: 0.0528 T23: 0.0118 REMARK 3 L TENSOR REMARK 3 L11: 2.1335 L22: 5.1585 REMARK 3 L33: 3.5052 L12: 1.5150 REMARK 3 L13: 0.9137 L23: 1.1946 REMARK 3 S TENSOR REMARK 3 S11: 0.0303 S12: 0.3033 S13: 0.2144 REMARK 3 S21: -0.3564 S22: -0.0511 S23: 0.0293 REMARK 3 S31: -0.4348 S32: -0.0523 S33: 0.0208 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 92 B 162 REMARK 3 ORIGIN FOR THE GROUP (A): -1.1200 11.1002 -19.1937 REMARK 3 T TENSOR REMARK 3 T11: 0.2112 T22: 0.1129 REMARK 3 T33: 0.1193 T12: -0.0766 REMARK 3 T13: 0.0167 T23: -0.0215 REMARK 3 L TENSOR REMARK 3 L11: 1.4423 L22: 2.6151 REMARK 3 L33: 5.2667 L12: -0.0350 REMARK 3 L13: -0.4220 L23: -1.2665 REMARK 3 S TENSOR REMARK 3 S11: 0.0555 S12: -0.0616 S13: -0.3840 REMARK 3 S21: 0.1817 S22: -0.0623 S23: 0.1332 REMARK 3 S31: 0.6087 S32: 0.1969 S33: 0.0068 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1 D 12 REMARK 3 ORIGIN FOR THE GROUP (A): -19.0327 -16.7158 5.5462 REMARK 3 T TENSOR REMARK 3 T11: 0.0489 T22: 0.1447 REMARK 3 T33: 0.0467 T12: -0.0626 REMARK 3 T13: 0.0194 T23: -0.0229 REMARK 3 L TENSOR REMARK 3 L11: 4.3789 L22: 3.3956 REMARK 3 L33: 2.6672 L12: 0.0552 REMARK 3 L13: -1.7127 L23: 0.8300 REMARK 3 S TENSOR REMARK 3 S11: -0.0899 S12: -0.1053 S13: -0.3371 REMARK 3 S21: 0.1536 S22: 0.0374 S23: 0.0220 REMARK 3 S31: 0.1759 S32: 0.0942 S33: 0.0525 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 12 REMARK 3 ORIGIN FOR THE GROUP (A): -19.3406 -15.4596 6.7377 REMARK 3 T TENSOR REMARK 3 T11: 0.0720 T22: 0.1505 REMARK 3 T33: 0.0952 T12: -0.0219 REMARK 3 T13: -0.0142 T23: -0.0044 REMARK 3 L TENSOR REMARK 3 L11: 5.8765 L22: 3.1565 REMARK 3 L33: 1.8385 L12: -2.2126 REMARK 3 L13: 0.8141 L23: 0.4461 REMARK 3 S TENSOR REMARK 3 S11: -0.2925 S12: -0.1689 S13: -0.1347 REMARK 3 S21: 0.1325 S22: 0.1474 S23: 0.0704 REMARK 3 S31: 0.1386 S32: 0.0725 S33: 0.1452 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : F 1 F 12 REMARK 3 ORIGIN FOR THE GROUP (A): -2.5348 25.7439 -23.6403 REMARK 3 T TENSOR REMARK 3 T11: 0.0204 T22: 0.1689 REMARK 3 T33: 0.0680 T12: -0.0355 REMARK 3 T13: 0.0134 T23: -0.0394 REMARK 3 L TENSOR REMARK 3 L11: 5.7195 L22: 2.3492 REMARK 3 L33: 1.9706 L12: 0.2250 REMARK 3 L13: 0.3179 L23: 0.4317 REMARK 3 S TENSOR REMARK 3 S11: -0.0263 S12: 0.0375 S13: 0.5236 REMARK 3 S21: -0.0157 S22: -0.0008 S23: 0.0588 REMARK 3 S31: -0.1253 S32: -0.0157 S33: 0.0270 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 1 E 12 REMARK 3 ORIGIN FOR THE GROUP (A): -2.6367 25.5056 -22.0011 REMARK 3 T TENSOR REMARK 3 T11: 0.0527 T22: 0.1582 REMARK 3 T33: 0.0797 T12: 0.0074 REMARK 3 T13: 0.0471 T23: -0.0683 REMARK 3 L TENSOR REMARK 3 L11: 6.4529 L22: 1.9790 REMARK 3 L33: 2.2131 L12: -0.8994 REMARK 3 L13: 1.0675 L23: -0.8955 REMARK 3 S TENSOR REMARK 3 S11: -0.0652 S12: -0.2544 S13: 0.0656 REMARK 3 S21: 0.0463 S22: -0.0237 S23: 0.0357 REMARK 3 S31: 0.0120 S32: -0.0315 S33: 0.0889 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: PHENIX.REFINE WAS USED AT INTERMEDIATE REMARK 3 STAGES OF REFINEMENT. COOT WAS USED FOR INTERACTIVE MODEL REMARK 3 BUILDING. MODEL GEOMETRY WAS ASSESSED ON THE MOLPROBITY SERVER. REMARK 4 REMARK 4 6C1Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1000231955. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97945 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14585 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 39.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.44900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PROTEIN COORDINATES FROM PDB ENTRY 3C2I. DNA REMARK 200 COORDINATES FROM A CURRENTLY UNPUBLISHED MODEL. REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3350, 0.1 M AMMONIUM SULFATE, REMARK 280 0.1 M TRIS, PH 8.5, VAPOR DIFFUSION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 3750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 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: 3660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, F, E 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 79 REMARK 465 SER A 80 REMARK 465 PRO A 81 REMARK 465 LYS A 82 REMARK 465 GLN A 83 REMARK 465 ARG A 84 REMARK 465 ARG A 85 REMARK 465 SER A 86 REMARK 465 ILE A 87 REMARK 465 ILE A 88 REMARK 465 ARG A 89 REMARK 465 ASP A 90 REMARK 465 ARG A 91 REMARK 465 GLY A 163 REMARK 465 SER A 164 REMARK 465 GLY B 79 REMARK 465 SER B 80 REMARK 465 PRO B 81 REMARK 465 LYS B 82 REMARK 465 GLN B 83 REMARK 465 ARG B 84 REMARK 465 ARG B 85 REMARK 465 SER B 86 REMARK 465 ILE B 87 REMARK 465 ILE B 88 REMARK 465 ARG B 89 REMARK 465 ASP B 90 REMARK 465 ARG B 91 REMARK 465 GLY B 163 REMARK 465 SER B 164 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 107 CD CE NZ REMARK 470 ARG A 115 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 119 CD CE NZ REMARK 470 GLN A 128 CD OE1 NE2 REMARK 470 ARG A 162 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 102 CG CD OE1 OE2 REMARK 470 LYS B 107 CD CE NZ REMARK 470 LYS B 109 CD CE NZ REMARK 470 LYS B 112 NZ REMARK 470 ARG B 115 NE CZ NH1 NH2 REMARK 470 GLN B 128 CD OE1 NE2 REMARK 470 LYS B 144 CD CE NZ REMARK 470 LEU B 150 CD1 CD2 REMARK 470 ARG B 162 CG CD NE CZ NH1 NH2 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 DC E 5 O3' 5CM E 6 P 0.074 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 GLN A 128 10.00 -69.16 REMARK 500 GLN B 128 11.75 -69.32 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 Di-nucleotide DC C 5 and 5CM C REMARK 800 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide 5CM C 6 and DG C REMARK 800 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide DC D 5 and 5CM D REMARK 800 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide 5CM D 6 and DG D REMARK 800 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide DC E 5 and 5CM E REMARK 800 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide 5CM E 6 and DG E REMARK 800 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide DC F 5 and 5CM F REMARK 800 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide 5CM F 6 and DG F REMARK 800 7 DBREF 6C1Y A 80 164 UNP P51608 MECP2_HUMAN 80 164 DBREF 6C1Y B 80 164 UNP P51608 MECP2_HUMAN 80 164 DBREF 6C1Y D 1 12 PDB 6C1Y 6C1Y 1 12 DBREF 6C1Y C 1 12 PDB 6C1Y 6C1Y 1 12 DBREF 6C1Y F 1 12 PDB 6C1Y 6C1Y 1 12 DBREF 6C1Y E 1 12 PDB 6C1Y 6C1Y 1 12 SEQADV 6C1Y GLY A 79 UNP P51608 EXPRESSION TAG SEQADV 6C1Y GLY B 79 UNP P51608 EXPRESSION TAG SEQRES 1 A 86 GLY SER PRO LYS GLN ARG ARG SER ILE ILE ARG ASP ARG SEQRES 2 A 86 GLY PRO MET TYR ASP ASP PRO THR LEU PRO GLU GLY TRP SEQRES 3 A 86 THR ARG LYS LEU LYS GLN ARG LYS SER GLY ARG SER ALA SEQRES 4 A 86 GLY LYS TYR ASP VAL TYR LEU ILE ASN PRO GLN GLY LYS SEQRES 5 A 86 ALA PHE ARG SER LYS VAL GLU LEU ILE ALA TYR PHE GLU SEQRES 6 A 86 LYS VAL GLY ASP THR SER LEU ASP PRO ASN ASP PHE ASP SEQRES 7 A 86 PHE THR VAL THR GLY ARG GLY SER SEQRES 1 B 86 GLY SER PRO LYS GLN ARG ARG SER ILE ILE ARG ASP ARG SEQRES 2 B 86 GLY PRO MET TYR ASP ASP PRO THR LEU PRO GLU GLY TRP SEQRES 3 B 86 THR ARG LYS LEU LYS GLN ARG LYS SER GLY ARG SER ALA SEQRES 4 B 86 GLY LYS TYR ASP VAL TYR LEU ILE ASN PRO GLN GLY LYS SEQRES 5 B 86 ALA PHE ARG SER LYS VAL GLU LEU ILE ALA TYR PHE GLU SEQRES 6 B 86 LYS VAL GLY ASP THR SER LEU ASP PRO ASN ASP PHE ASP SEQRES 7 B 86 PHE THR VAL THR GLY ARG GLY SER SEQRES 1 D 12 DG DC DC DA DC 5CM DG DG DT DG DG DC SEQRES 1 C 12 DG DC DC DA DC 5CM DG DG DT DG DG DC SEQRES 1 F 12 DG DC DC DA DC 5CM DG DG DT DG DG DC SEQRES 1 E 12 DG DC DC DA DC 5CM DG DG DT DG DG DC HET 5CM D 6 20 HET 5CM C 6 20 HET 5CM F 6 20 HET 5CM E 6 20 HET UNX A 201 1 HET UNX B 201 1 HET UNX B 202 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 3(X) HELIX 1 AA1 SER A 134 GLY A 146 1 13 HELIX 2 AA2 ASP A 151 PHE A 155 5 5 HELIX 3 AA3 SER B 134 GLY B 146 1 13 HELIX 4 AA4 ASP B 151 PHE B 155 5 5 SHEET 1 AA1 3 THR A 105 GLN A 110 0 SHEET 2 AA1 3 TYR A 120 ILE A 125 -1 O ILE A 125 N THR A 105 SHEET 3 AA1 3 ALA A 131 PHE A 132 -1 O PHE A 132 N LEU A 124 SHEET 1 AA2 3 THR B 105 GLN B 110 0 SHEET 2 AA2 3 TYR B 120 ILE B 125 -1 O ILE B 125 N THR B 105 SHEET 3 AA2 3 ALA B 131 PHE B 132 -1 O PHE B 132 N LEU B 124 LINK O3' DC D 5 P 5CM D 6 1555 1555 1.54 LINK O3' 5CM D 6 P DG D 7 1555 1555 1.61 LINK O3' DC C 5 P 5CM C 6 1555 1555 1.64 LINK O3' 5CM C 6 P DG C 7 1555 1555 1.58 LINK O3' DC F 5 P 5CM F 6 1555 1555 1.58 LINK O3' 5CM F 6 P DG F 7 1555 1555 1.64 LINK O3' DC E 5 P 5CM E 6 1555 1555 1.68 LINK O3' 5CM E 6 P DG E 7 1555 1555 1.57 SITE 1 AC1 12 LYS A 109 ARG A 111 LYS A 112 SER A 113 SITE 2 AC1 12 SER A 116 ASP A 121 TYR A 123 ARG A 133 SITE 3 AC1 12 DA C 4 DG C 7 DG D 7 DG D 8 SITE 1 AC2 14 ARG A 111 LYS A 112 SER A 113 GLY A 114 SITE 2 AC2 14 ARG A 115 SER A 116 ASP A 121 ARG A 133 SITE 3 AC2 14 DC C 5 DG C 8 DC D 5 5CM D 6 SITE 4 AC2 14 DG D 7 DG D 8 SITE 1 AC3 8 ARG A 133 SER A 134 GLN B 110 LYS B 112 SITE 2 AC3 8 DG C 7 DG C 8 DA D 4 DG D 7 SITE 1 AC4 11 ARG A 133 SER A 134 TYR B 95 GLN B 110 SITE 2 AC4 11 LYS B 112 TYR B 120 DC C 5 5CM C 6 SITE 3 AC4 11 DG C 7 DC D 5 DG D 8 SITE 1 AC5 9 ARG B 111 LYS B 112 SER B 113 SER B 116 SITE 2 AC5 9 ASP B 121 DA E 4 DG E 7 DG F 7 SITE 3 AC5 9 DG F 8 SITE 1 AC6 12 ARG B 111 LYS B 112 SER B 113 GLY B 114 SITE 2 AC6 12 ARG B 115 SER B 116 ASP B 121 DC E 5 SITE 3 AC6 12 DG E 8 5CM F 6 DG F 7 DG F 8 SITE 1 AC7 10 GLN A 110 LYS A 112 ARG B 133 SER B 134 SITE 2 AC7 10 VAL B 136 PHE B 157 DG E 7 DG E 8 SITE 3 AC7 10 DA F 4 DG F 7 SITE 1 AC8 13 TYR A 95 GLN A 110 LYS A 112 TYR A 120 SITE 2 AC8 13 ARG B 133 SER B 134 VAL B 136 DC E 5 SITE 3 AC8 13 5CM E 6 DG E 7 DG E 8 DC F 5 SITE 4 AC8 13 DG F 8 CRYST1 40.753 47.359 54.623 68.15 89.83 65.98 P 1 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 0.024538 -0.010935 0.004779 0.00000 SCALE2 0.000000 0.023117 -0.010276 0.00000 SCALE3 0.000000 0.000000 0.020035 0.00000