PDB Short entry for 6OGK HEADER DNA BINDING PROTEIN/DNA 02-APR-19 6OGK TITLE MECP2 MBD IN COMPLEX WITH DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYL-CPG-BINDING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MECP2; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*GP*CP*CP*TP*AP*(5CM)P*AP*CP*TP*CP*CP*G)-3'); COMPND 8 CHAIN: D; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'-D(*CP*GP*GP*AP*GP*TP*GP*TP*AP*GP*GP*C)-3'); COMPND 12 CHAIN: C; 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: MECP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-V2R-RIL; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PNIC-CH; 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 MBD, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, DNA KEYWDS 2 BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.LEI,W.TEMPEL,C.H.ARROWSMITH,C.BOUNTRA,A.M.EDWARDS,J.MIN,STRUCTURAL AUTHOR 2 GENOMICS CONSORTIUM,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 3 11-OCT-23 6OGK 1 LINK REVDAT 2 20-NOV-19 6OGK 1 JRNL REVDAT 1 01-MAY-19 6OGK 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. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 15648 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) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1773 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1141 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.3390 REMARK 3 BIN FREE R VALUE SET COUNT : 139 REMARK 3 BIN FREE R VALUE : 0.3650 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 585 REMARK 3 NUCLEIC ACID ATOMS : 487 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 56 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.67000 REMARK 3 B22 (A**2) : -1.75000 REMARK 3 B33 (A**2) : 1.08000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.125 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.119 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.099 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.003 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1159 ; 0.011 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 805 ; 0.003 ; 0.018 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1678 ; 1.743 ; 1.445 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1883 ; 1.524 ; 2.085 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 75 ; 6.407 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 32 ;29.027 ;22.188 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 91 ;13.015 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;24.813 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 150 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 990 ; 0.018 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 262 ; 0.008 ; 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): 303 ; 1.036 ; 1.947 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 302 ; 1.037 ; 1.943 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 377 ; 1.649 ; 2.905 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 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 90 A 165 REMARK 3 ORIGIN FOR THE GROUP (A): 18.9121 4.7036 6.8900 REMARK 3 T TENSOR REMARK 3 T11: 0.0098 T22: 0.0475 REMARK 3 T33: 0.0124 T12: 0.0057 REMARK 3 T13: -0.0048 T23: -0.0203 REMARK 3 L TENSOR REMARK 3 L11: 1.2305 L22: 3.8901 REMARK 3 L33: 3.8538 L12: -0.1874 REMARK 3 L13: 0.1671 L23: -1.4131 REMARK 3 S TENSOR REMARK 3 S11: 0.0335 S12: 0.1408 S13: -0.0986 REMARK 3 S21: -0.1774 S22: 0.0605 S23: 0.0330 REMARK 3 S31: 0.0492 S32: 0.0080 S33: -0.0939 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 : D 1 D 12 REMARK 3 ORIGIN FOR THE GROUP (A): 19.2156 7.9129 22.1422 REMARK 3 T TENSOR REMARK 3 T11: 0.0264 T22: 0.1730 REMARK 3 T33: 0.0915 T12: 0.0298 REMARK 3 T13: 0.0092 T23: 0.0829 REMARK 3 L TENSOR REMARK 3 L11: 3.7879 L22: 2.7477 REMARK 3 L33: 2.6501 L12: -2.4782 REMARK 3 L13: -2.0576 L23: 0.0756 REMARK 3 S TENSOR REMARK 3 S11: -0.2685 S12: -0.2671 S13: -0.0791 REMARK 3 S21: 0.0821 S22: 0.2271 S23: -0.0301 REMARK 3 S31: 0.2030 S32: -0.0651 S33: 0.0413 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 : C 1 C 12 REMARK 3 ORIGIN FOR THE GROUP (A): 20.1600 9.4688 21.9732 REMARK 3 T TENSOR REMARK 3 T11: 0.0270 T22: 0.0882 REMARK 3 T33: 0.0514 T12: -0.0356 REMARK 3 T13: -0.0213 T23: 0.0186 REMARK 3 L TENSOR REMARK 3 L11: 6.6317 L22: 3.4296 REMARK 3 L33: 2.3318 L12: -0.4082 REMARK 3 L13: 2.0605 L23: -0.5483 REMARK 3 S TENSOR REMARK 3 S11: -0.1509 S12: -0.0369 S13: 0.4735 REMARK 3 S21: 0.1083 S22: 0.0891 S23: -0.0688 REMARK 3 S31: -0.0933 S32: -0.0830 S33: 0.0618 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 6OGK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-APR-19. REMARK 100 THE DEPOSITION ID IS D_1000236100. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-SEP-18 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 : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97741 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18969 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 40.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 1.83500 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: PDB ENTRY 6C1Y REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50% PRECIPITANT MIX 4, 0.1M BUFFER REMARK 280 SYSTEM 1, 0.06M DIVALENTS (MORPHEUS A4), PH 6.5, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 20.23500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.15200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.98800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.15200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.23500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.98800 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 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 ALA A 77 REMARK 465 SER A 78 REMARK 465 ALA 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 SER A 166 REMARK 465 ARG A 167 REMARK 465 ALA A 168 REMARK 465 ALA A 169 REMARK 465 HIS A 170 REMARK 465 HIS A 171 REMARK 465 HIS A 172 REMARK 465 HIS A 173 REMARK 465 HIS A 174 REMARK 465 HIS A 175 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 ARG A 91 CG CD NE CZ NH1 NH2 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 LYS A 135 CE NZ REMARK 470 LYS A 144 NZ 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 D 11 N1 DC D 11 C6 0.040 REMARK 500 DC D 11 C4 DC D 11 C5 0.068 REMARK 500 DG C 5 O3' DT C 6 P -0.076 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DG D 1 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 211 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 144 O REMARK 620 2 ASP A 154 O 16.2 REMARK 620 3 ASP A 154 OD1 16.9 6.6 REMARK 620 4 HOH A 304 O 20.4 4.2 7.5 REMARK 620 5 HOH A 309 O 15.7 1.7 8.1 5.2 REMARK 620 6 HOH A 324 O 22.6 6.7 7.9 2.9 8.0 REMARK 620 7 HOH A 327 O 20.7 7.7 3.9 6.4 9.3 5.3 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 211 DBREF 6OGK A 77 167 UNP P51608 MECP2_HUMAN 77 167 DBREF 6OGK D 1 12 PDB 6OGK 6OGK 1 12 DBREF 6OGK C 1 12 PDB 6OGK 6OGK 1 12 SEQADV 6OGK ALA A 168 UNP P51608 EXPRESSION TAG SEQADV 6OGK ALA A 169 UNP P51608 EXPRESSION TAG SEQADV 6OGK HIS A 170 UNP P51608 EXPRESSION TAG SEQADV 6OGK HIS A 171 UNP P51608 EXPRESSION TAG SEQADV 6OGK HIS A 172 UNP P51608 EXPRESSION TAG SEQADV 6OGK HIS A 173 UNP P51608 EXPRESSION TAG SEQADV 6OGK HIS A 174 UNP P51608 EXPRESSION TAG SEQADV 6OGK HIS A 175 UNP P51608 EXPRESSION TAG SEQRES 1 A 99 ALA SER ALA SER PRO LYS GLN ARG ARG SER ILE ILE ARG SEQRES 2 A 99 ASP ARG GLY PRO MET TYR ASP ASP PRO THR LEU PRO GLU SEQRES 3 A 99 GLY TRP THR ARG LYS LEU LYS GLN ARG LYS SER GLY ARG SEQRES 4 A 99 SER ALA GLY LYS TYR ASP VAL TYR LEU ILE ASN PRO GLN SEQRES 5 A 99 GLY LYS ALA PHE ARG SER LYS VAL GLU LEU ILE ALA TYR SEQRES 6 A 99 PHE GLU LYS VAL GLY ASP THR SER LEU ASP PRO ASN ASP SEQRES 7 A 99 PHE ASP PHE THR VAL THR GLY ARG GLY SER PRO SER ARG SEQRES 8 A 99 ALA ALA HIS HIS HIS HIS HIS HIS SEQRES 1 D 12 DG DC DC DT DA 5CM DA DC DT DC DC DG SEQRES 1 C 12 DC DG DG DA DG DT DG DT DA DG DG DC HET 5CM D 6 20 HET UNX A 201 1 HET UNX A 202 1 HET UNX A 203 1 HET UNX A 204 1 HET UNX A 205 1 HET UNX A 206 1 HET UNX A 207 1 HET UNX A 208 1 HET UNX A 209 1 HET UNX A 210 1 HET CA A 211 1 HET UNX D 101 1 HET UNX D 102 1 HET UNX D 103 1 HET UNX D 104 1 HET UNX D 105 1 HET UNX C 101 1 HET UNX C 102 1 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM UNX UNKNOWN ATOM OR ION HETNAM CA CALCIUM ION FORMUL 2 5CM C10 H16 N3 O7 P FORMUL 4 UNX 17(X) FORMUL 14 CA CA 2+ FORMUL 22 HOH *56(H2 O) HELIX 1 AA1 SER A 134 VAL A 145 1 12 HELIX 2 AA2 ASP A 151 PHE A 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 TYR A 123 N LYS A 107 SHEET 3 AA1 3 ALA A 131 PHE A 132 -1 O PHE A 132 N LEU A 124 LINK O3' DA D 5 P 5CM D 6 1555 1555 1.56 LINK O3' 5CM D 6 P DA D 7 1555 1555 1.67 LINK O LYS A 144 CA CA A 211 1555 4555 2.23 LINK O ASP A 154 CA CA A 211 1555 1555 2.38 LINK OD1 ASP A 154 CA CA A 211 1555 1555 2.29 LINK CA CA A 211 O HOH A 304 1555 1555 2.39 LINK CA CA A 211 O HOH A 309 1555 1555 2.09 LINK CA CA A 211 O HOH A 324 1555 1555 2.58 LINK CA CA A 211 O HOH A 327 1555 1555 2.39 SITE 1 AC1 6 LYS A 144 ASP A 154 HOH A 304 HOH A 309 SITE 2 AC1 6 HOH A 324 HOH A 327 CRYST1 40.470 51.976 66.304 90.00 90.00 90.00 P 21 21 21 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 0.024710 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019240 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015082 0.00000