PDB Short entry for 3QMB HEADER DNA BINDING PROTEIN/DNA 04-FEB-11 3QMB 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, RESIDUES 161-222; 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: 5'-D(*GP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*C)-3'; COMPND 10 CHAIN: B, C; COMPND 11 FRAGMENT: DNA (NONMETHYLATED CPG ISLAND); COMPND 12 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: CFP1, CGBP, CXXC1, PCCX1, PHF18; 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. 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 5 21-FEB-24 3QMB 1 REMARK SEQADV LINK REVDAT 4 08-NOV-17 3QMB 1 REMARK REVDAT 3 30-MAR-11 3QMB 1 JRNL REVDAT 2 16-MAR-11 3QMB 1 JRNL REVDAT 1 23-FEB-11 3QMB 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. 2.06 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REFMAC_5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.06 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 10037 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) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 497 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) : 2.06 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.11 REMARK 3 REFLECTION IN BIN (WORKING SET) : 661 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.50 REMARK 3 BIN R VALUE (WORKING SET) : 0.2650 REMARK 3 BIN FREE R VALUE SET COUNT : 39 REMARK 3 BIN FREE R VALUE : 0.2710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 420 REMARK 3 NUCLEIC ACID ATOMS : 486 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 18 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.51000 REMARK 3 B22 (A**2) : -0.39000 REMARK 3 B33 (A**2) : -0.12000 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): 0.153 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.156 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.446 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.933 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 968 ; 0.010 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1396 ; 1.709 ; 2.579 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 53 ; 5.453 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 23 ;31.868 ;20.435 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 81 ;15.839 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;21.093 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 148 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 581 ; 0.007 ; 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): 266 ; 0.570 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 414 ; 1.085 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 702 ; 1.825 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 982 ; 2.838 ; 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): 6.5590 11.1440 20.4580 REMARK 3 T TENSOR REMARK 3 T11: 0.1635 T22: 0.1613 REMARK 3 T33: -0.0311 T12: -0.0194 REMARK 3 T13: -0.0271 T23: -0.0065 REMARK 3 L TENSOR REMARK 3 L11: 5.7929 L22: 2.8489 REMARK 3 L33: 6.6538 L12: 0.4597 REMARK 3 L13: -0.0323 L23: -2.5780 REMARK 3 S TENSOR REMARK 3 S11: -0.1583 S12: -0.2613 S13: 0.0289 REMARK 3 S21: 0.1939 S22: 0.1087 S23: 0.0213 REMARK 3 S31: -0.6137 S32: 0.0420 S33: 0.0496 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): 9.3310 10.3990 7.3790 REMARK 3 T TENSOR REMARK 3 T11: 0.3657 T22: 0.1916 REMARK 3 T33: 0.0687 T12: -0.1870 REMARK 3 T13: 0.0172 T23: -0.0010 REMARK 3 L TENSOR REMARK 3 L11: 2.1524 L22: 10.6057 REMARK 3 L33: 1.5864 L12: 3.0791 REMARK 3 L13: 1.5403 L23: 0.0607 REMARK 3 S TENSOR REMARK 3 S11: 0.1765 S12: -0.1373 S13: 0.1711 REMARK 3 S21: 0.0490 S22: -0.3498 S23: 0.4154 REMARK 3 S31: -0.0974 S32: 0.1758 S33: 0.1733 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): 8.2350 11.4110 6.5630 REMARK 3 T TENSOR REMARK 3 T11: 0.4868 T22: 0.3654 REMARK 3 T33: 0.2651 T12: -0.1595 REMARK 3 T13: -0.0435 T23: 0.0018 REMARK 3 L TENSOR REMARK 3 L11: 3.5780 L22: 4.6369 REMARK 3 L33: 2.9449 L12: 3.1224 REMARK 3 L13: 0.9485 L23: 0.9050 REMARK 3 S TENSOR REMARK 3 S11: -0.0944 S12: -0.4101 S13: 0.4118 REMARK 3 S21: -0.6611 S22: -0.2409 S23: 0.6237 REMARK 3 S31: -0.1680 S32: 0.2560 S33: 0.3353 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 3QMB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-FEB-11. REMARK 100 THE DEPOSITION ID IS D_1000063824. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUN-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) : 0.97904 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 : 10064 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.500 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : 0.50600 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: SAD REMARK 200 SOFTWARE USED: SHARP, DM 6.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 7.5, 0.2M CACL2, 28% REMARK 280 PEG400, 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 57.80000 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 57.80000 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 18.68750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.98250 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 18.68750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.98250 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 57.80000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 18.68750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 35.98250 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 57.80000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 18.68750 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 35.98250 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: 2640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 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 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 ARG A 168 CG CD NE CZ NH1 NH2 REMARK 470 SER A 169 OG 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 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 DG B 10 O4' - C1' - N9 ANGL. DEV. = -5.9 DEGREES REMARK 500 DC B 12 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC C 2 O4' - C1' - N1 ANGL. DEV. = -4.6 DEGREES REMARK 500 DC C 3 O4' - C1' - N1 ANGL. DEV. = -4.4 DEGREES REMARK 500 DA C 4 O4' - C1' - N9 ANGL. DEV. = -4.7 DEGREES REMARK 500 DC C 5 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG C 10 O4' - C1' - N9 ANGL. DEV. = -6.4 DEGREES REMARK 500 DC C 12 O4' - C1' - N1 ANGL. DEV. = 2.7 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 SER A 169 -167.16 -122.30 REMARK 500 CYS A 207 132.98 -37.80 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 173 SG REMARK 620 2 CYS A 176 SG 112.0 REMARK 620 3 CYS A 179 SG 116.1 106.7 REMARK 620 4 CYS A 212 SG 105.0 118.6 98.2 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 185 SG REMARK 620 2 CYS A 188 SG 110.1 REMARK 620 3 CYS A 191 SG 118.3 101.8 REMARK 620 4 CYS A 207 SG 109.3 117.2 100.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 13 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 11 O6 REMARK 620 2 HOH B 14 O 150.6 REMARK 620 3 HOH B 16 O 90.2 83.0 REMARK 620 4 HOH B 17 O 82.2 96.2 163.1 REMARK 620 5 HOH C 13 O 70.2 139.0 97.3 94.4 REMARK 620 N 1 2 3 4 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 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 13 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3QMC RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH A DIFFERENT UNMETHYLATED CPG DNA. REMARK 900 RELATED ID: 3QMD 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 RELATED ID: 3QMH RELATED DB: PDB REMARK 900 RELATED ID: 3QMI RELATED DB: PDB DBREF 3QMB A 165 226 UNP Q9P0U4 CXXC1_HUMAN 161 222 DBREF 3QMB B 1 12 PDB 3QMB 3QMB 1 12 DBREF 3QMB C 1 12 PDB 3QMB 3QMB 1 12 SEQADV 3QMB MET A 148 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMB HIS A 149 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMB HIS A 150 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMB HIS A 151 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMB HIS A 152 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMB HIS A 153 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMB HIS A 154 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMB SER A 155 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMB SER A 156 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMB ARG A 157 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMB GLU A 158 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMB ASN A 159 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMB LEU A 160 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMB TYR A 161 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMB PHE A 162 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMB GLN A 163 UNP Q9P0U4 EXPRESSION TAG SEQADV 3QMB 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 DC DC DG DG DT DG DG DC SEQRES 1 C 12 DG DC DC DA DC DC DG DG DT DG DG DC HET ZN A 300 1 HET ZN A 301 1 HET CA B 13 1 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION FORMUL 4 ZN 2(ZN 2+) FORMUL 6 CA CA 2+ FORMUL 7 HOH *18(H2 O) HELIX 1 1 CYS A 188 MET A 194 1 7 HELIX 2 2 LYS A 195 GLY A 198 5 4 HELIX 3 3 CYS A 207 GLN A 211 5 5 HELIX 4 4 ARG A 217 LYS A 221 5 5 LINK SG CYS A 173 ZN ZN A 300 1555 1555 2.36 LINK SG CYS A 176 ZN ZN A 300 1555 1555 2.36 LINK SG CYS A 179 ZN ZN A 300 1555 1555 2.44 LINK SG CYS A 185 ZN ZN A 301 1555 1555 2.34 LINK SG CYS A 188 ZN ZN A 301 1555 1555 2.38 LINK SG CYS A 191 ZN ZN A 301 1555 1555 2.39 LINK SG CYS A 207 ZN ZN A 301 1555 1555 2.30 LINK SG CYS A 212 ZN ZN A 300 1555 1555 2.33 LINK O6 DG B 11 CA CA B 13 1555 1555 2.71 LINK CA CA B 13 O HOH B 14 1555 1555 2.46 LINK CA CA B 13 O HOH B 16 1555 1555 2.41 LINK CA CA B 13 O HOH B 17 1555 1555 2.60 LINK CA CA B 13 O HOH C 13 1555 1555 2.54 SITE 1 AC1 4 CYS A 173 CYS A 176 CYS A 179 CYS A 212 SITE 1 AC2 5 CYS A 185 GLY A 186 CYS A 188 CYS A 191 SITE 2 AC2 5 CYS A 207 SITE 1 AC3 6 DG B 10 DG B 11 HOH B 14 HOH B 16 SITE 2 AC3 6 HOH B 17 HOH C 13 CRYST1 37.375 71.965 115.600 90.00 90.00 90.00 C 2 2 21 16 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 0.026756 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013896 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008651 0.00000