HEADER DNA BINDING PROTEIN/DNA 04-FEB-11 3QMD TITLE STRUCTURAL BASIS OF SELECTIVE BINDING OF NONMETHYLATED CPG ISLANDS BY TITLE 2 THE CXXC DOMAIN OF CFP1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CPG-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CXXC-TYPE ZN FINGER; COMPND 5 SYNONYM: CXXC-TYPE ZINC FINGER PROTEIN 1, PHD FINGER AND CXXC DOMAIN- COMPND 6 CONTAINING PROTEIN 1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*AP*TP*GP*GP*C)-3'); COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: DNA (NONMETHYLATED CPG ISLAND); COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*GP*CP*CP*AP*TP*CP*GP*TP*TP*GP*GP*C)-3'); COMPND 15 CHAIN: C; COMPND 16 FRAGMENT: DNA (NONMETHYLATED CPG ISLAND); COMPND 17 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: CXXC1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-(DE3)-V2R-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28-MHL; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: DNA WAS PURCHASED FROM INTEGRATED DNA TECHNOLOGIES, SOURCE 14 INC.; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 OTHER_DETAILS: DNA WAS PURCHASED FROM INTEGRATED DNA TECHNOLOGIES, SOURCE 18 INC. KEYWDS STRUCTURAL GENOMICS CONSORTIUM, SGC, CXXC-TYPE ZN FINGER, DNA KEYWDS 2 BINDING, UNMETHYLATED CPG MOTIFS, NUCLEUS SPECKLE, DNA BINDING KEYWDS 3 PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.LAM,C.XU,C.B.BIAN,J.KANIA,C.BOUNTRA,J.WEIGELT,C.H.ARROWSMITH, AUTHOR 2 A.M.EDWARDS,A.BOCHKAREV,J.MIN,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 4 08-NOV-17 3QMD 1 REMARK REVDAT 3 30-MAR-11 3QMD 1 JRNL REMARK REVDAT 2 16-MAR-11 3QMD 1 JRNL REVDAT 1 23-FEB-11 3QMD 0 JRNL AUTH C.XU,C.BIAN,R.LAM,A.DONG,J.MIN JRNL TITL THE STRUCTURAL BASIS FOR SELECTIVE BINDING OF NON-METHYLATED JRNL TITL 2 CPG ISLANDS BY THE CFP1 CXXC DOMAIN. JRNL REF NAT COMMUN V. 2 227 2011 JRNL REFN ESSN 2041-1723 JRNL PMID 21407193 JRNL DOI 10.1038/NCOMMS1237 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REFMAC_5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.11 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 11585 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 545 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 693 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.66 REMARK 3 BIN R VALUE (WORKING SET) : 0.2930 REMARK 3 BIN FREE R VALUE SET COUNT : 42 REMARK 3 BIN FREE R VALUE : 0.2850 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 412 REMARK 3 NUCLEIC ACID ATOMS : 486 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 26 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.11000 REMARK 3 B22 (A**2) : -0.24000 REMARK 3 B33 (A**2) : 0.35000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.136 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.123 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.899 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 969 ; 0.011 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1398 ; 1.662 ; 2.577 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 54 ; 5.384 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 23 ;32.722 ;19.565 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 83 ;15.918 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;22.081 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 148 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 582 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 264 ; 0.649 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 413 ; 1.185 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 705 ; 1.899 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 984 ; 3.057 ; 4.500 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 -10 A 9999 REMARK 3 ORIGIN FOR THE GROUP (A): -4.2410 10.6130 -21.7700 REMARK 3 T TENSOR REMARK 3 T11: 0.0510 T22: 0.3022 REMARK 3 T33: 0.0493 T12: 0.0424 REMARK 3 T13: 0.0261 T23: 0.0255 REMARK 3 L TENSOR REMARK 3 L11: 5.3842 L22: 1.4143 REMARK 3 L33: 7.3494 L12: -0.1802 REMARK 3 L13: -1.7590 L23: 1.2607 REMARK 3 S TENSOR REMARK 3 S11: 0.0985 S12: 0.1198 S13: 0.2526 REMARK 3 S21: 0.0034 S22: 0.2186 S23: 0.0224 REMARK 3 S31: -0.2963 S32: -0.0822 S33: -0.3170 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 -10 B 9999 REMARK 3 ORIGIN FOR THE GROUP (A): -4.6540 11.7850 -8.4860 REMARK 3 T TENSOR REMARK 3 T11: 0.3158 T22: 0.2533 REMARK 3 T33: 0.1085 T12: 0.1396 REMARK 3 T13: 0.0262 T23: -0.0118 REMARK 3 L TENSOR REMARK 3 L11: 3.7652 L22: 16.7329 REMARK 3 L33: 4.2438 L12: -4.6573 REMARK 3 L13: 1.1861 L23: 1.4551 REMARK 3 S TENSOR REMARK 3 S11: 0.3824 S12: 0.1749 S13: 0.0577 REMARK 3 S21: 0.0923 S22: -0.6638 S23: -0.0610 REMARK 3 S31: -0.2990 S32: -0.0669 S33: 0.2814 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 -10 C 9999 REMARK 3 ORIGIN FOR THE GROUP (A): -3.4600 12.2960 -7.8380 REMARK 3 T TENSOR REMARK 3 T11: 0.7334 T22: 0.4555 REMARK 3 T33: 0.2022 T12: 0.1048 REMARK 3 T13: -0.0761 T23: 0.1270 REMARK 3 L TENSOR REMARK 3 L11: 5.6596 L22: 10.1835 REMARK 3 L33: 7.7618 L12: -1.8769 REMARK 3 L13: 3.7454 L23: -5.7504 REMARK 3 S TENSOR REMARK 3 S11: 0.2281 S12: 1.2388 S13: 0.6852 REMARK 3 S21: 1.9729 S22: -0.7137 S23: -1.0163 REMARK 3 S31: 0.2644 S32: -0.5596 S33: 0.4856 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3QMD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-FEB-11. REMARK 100 THE DEPOSITION ID IS D_1000063826. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-AUG-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 0.97924 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : ROSENBAUM-ROCK HIGH-RESOLUTION REMARK 200 DOUBLE-CRYSTAL MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11621 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.51200 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.1.4 REMARK 200 STARTING MODEL: PDB 3QMB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 7.5, 0.1M MGCL2, 30% REMARK 280 PEG550MME., VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 62.88450 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 62.88450 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 15.32650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.34400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 15.32650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.34400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 62.88450 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 15.32650 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 37.34400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 62.88450 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 15.32650 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 37.34400 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: 2360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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 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 MET A 148 REMARK 465 HIS A 149 REMARK 465 HIS A 150 REMARK 465 HIS A 151 REMARK 465 HIS A 152 REMARK 465 HIS A 153 REMARK 465 HIS A 154 REMARK 465 SER A 155 REMARK 465 SER A 156 REMARK 465 ARG A 157 REMARK 465 GLU A 158 REMARK 465 ASN A 159 REMARK 465 LEU A 160 REMARK 465 TYR A 161 REMARK 465 PHE A 162 REMARK 465 GLN A 163 REMARK 465 GLY A 164 REMARK 465 GLN A 165 REMARK 465 ILE A 166 REMARK 465 LYS A 167 REMARK 465 ARG A 168 REMARK 465 TYR A 222 REMARK 465 PHE A 223 REMARK 465 PRO A 224 REMARK 465 SER A 225 REMARK 465 SER A 226 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 GLU A 177 CG CD OE1 OE2 REMARK 470 LYS A 195 CG CD CE NZ REMARK 470 LYS A 202 CG CD CE NZ REMARK 470 GLU A 218 CG CD OE1 OE2 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 B 3 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 DA B 8 O4' - C1' - N9 ANGL. DEV. = -5.5 DEGREES REMARK 500 DT B 9 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG B 10 O4' - C1' - N9 ANGL. DEV. = -5.4 DEGREES REMARK 500 DA C 4 O4' - C1' - N9 ANGL. DEV. = -5.1 DEGREES REMARK 500 DT C 5 C3' - C2' - C1' ANGL. DEV. = -5.8 DEGREES REMARK 500 DC C 6 O5' - P - OP1 ANGL. DEV. = 8.5 DEGREES REMARK 500 DC C 12 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES 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 ZN A 300 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 176 SG REMARK 620 2 CYS A 212 SG 117.7 REMARK 620 3 CYS A 173 SG 108.4 104.9 REMARK 620 4 CYS A 179 SG 106.2 101.6 118.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 188 SG REMARK 620 2 CYS A 191 SG 104.8 REMARK 620 3 CYS A 207 SG 119.1 101.5 REMARK 620 4 CYS A 185 SG 108.2 118.2 105.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3QMB RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH A DIFFERENT UNMETHYLATED CPG DNA. REMARK 900 RELATED ID: 3QMC RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH A DIFFERENT UNMETHYLATED CPG DNA. REMARK 900 RELATED ID: 3QMG RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH A DIFFERENT UNMETHYLATED CPG DNA. REMARK 900 RELATED ID: 3QMH RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH A DIFFERENT UNMETHYLATED CPG DNA. REMARK 900 RELATED ID: 3QMI RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH A DIFFERENT UNMETHYLATED CPG DNA. DBREF 3QMD A 165 226 UNP Q9P0U4 CXXC1_HUMAN 161 222 DBREF 3QMD B 1 12 PDB 3QMD 3QMD 1 12 DBREF 3QMD C 1 12 PDB 3QMD 3QMD 1 12 SEQADV 3QMD MET A 148 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMD HIS A 149 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMD HIS A 150 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMD HIS A 151 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMD HIS A 152 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMD HIS A 153 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMD HIS A 154 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMD SER A 155 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMD SER A 156 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMD ARG A 157 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMD GLU A 158 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMD ASN A 159 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMD LEU A 160 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMD TYR A 161 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMD PHE A 162 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMD GLN A 163 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMD GLY A 164 UNP Q9P0U4 EXPRESSION TAG SEQRES 1 A 79 MET HIS HIS HIS HIS HIS HIS SER SER ARG GLU ASN LEU SEQRES 2 A 79 TYR PHE GLN GLY GLN ILE LYS ARG SER ALA ARG MET CYS SEQRES 3 A 79 GLY GLU CYS GLU ALA CYS ARG ARG THR GLU ASP CYS GLY SEQRES 4 A 79 HIS CYS ASP PHE CYS ARG ASP MET LYS LYS PHE GLY GLY SEQRES 5 A 79 PRO ASN LYS ILE ARG GLN LYS CYS ARG LEU ARG GLN CYS SEQRES 6 A 79 GLN LEU ARG ALA ARG GLU SER TYR LYS TYR PHE PRO SER SEQRES 7 A 79 SER SEQRES 1 B 12 DG DC DC DA DA DC DG DA DT DG DG DC SEQRES 1 C 12 DG DC DC DA DT DC DG DT DT DG DG DC HET ZN A 300 1 HET ZN A 301 1 HETNAM ZN ZINC ION FORMUL 4 ZN 2(ZN 2+) FORMUL 6 HOH *26(H2 O) HELIX 1 1 CYS A 176 ARG A 181 1 6 HELIX 2 2 CYS A 188 MET A 194 1 7 HELIX 3 3 LYS A 195 GLY A 198 5 4 HELIX 4 4 CYS A 207 GLN A 211 5 5 HELIX 5 5 ARG A 217 LYS A 221 5 5 LINK SG CYS A 176 ZN ZN A 300 1555 1555 2.33 LINK SG CYS A 188 ZN ZN A 301 1555 1555 2.34 LINK SG CYS A 191 ZN ZN A 301 1555 1555 2.34 LINK SG CYS A 207 ZN ZN A 301 1555 1555 2.36 LINK SG CYS A 185 ZN ZN A 301 1555 1555 2.38 LINK SG CYS A 212 ZN ZN A 300 1555 1555 2.39 LINK SG CYS A 173 ZN ZN A 300 1555 1555 2.43 LINK SG CYS A 179 ZN ZN A 300 1555 1555 2.47 SITE 1 AC1 4 CYS A 173 CYS A 176 CYS A 179 CYS A 212 SITE 1 AC2 4 CYS A 185 CYS A 188 CYS A 191 CYS A 207 CRYST1 30.653 74.688 125.769 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 0.032623 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013389 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007951 0.00000