HEADER DNA 22-AUG-12 4GQD TITLE DNA HOLLIDAY JUNCTION STABILIZED BY CHLORINE HALOGEN BOND. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*CP*GP*GP*TP*AP*(UCL)P*CP*GP*G)-3'); COMPND 3 CHAIN: A, D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3'); COMPND 7 CHAIN: B, C; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHETICALLY ENGINEERED DNA SEQUENCE; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: SYNTHETICALLY ENGINEERED DNA SEQUENCE KEYWDS DNA HOLLIDAY JUNCTION, HALOGEN BOND, DNA EXPDTA X-RAY DIFFRACTION AUTHOR M.CARTER,P.S.HO REVDAT 3 13-SEP-23 4GQD 1 REMARK LINK REVDAT 2 18-DEC-13 4GQD 1 JRNL REVDAT 1 31-JUL-13 4GQD 0 JRNL AUTH M.CARTER,A.R.VOTH,M.R.SCHOLFIELD,B.RUMMEL,L.C.SOWERS,P.S.HO JRNL TITL ENTHALPY-ENTROPY COMPENSATION IN BIOMOLECULAR HALOGEN BONDS JRNL TITL 2 MEASURED IN DNA JUNCTIONS. JRNL REF BIOCHEMISTRY V. 52 4891 2013 JRNL REFN ISSN 0006-2960 JRNL PMID 23789744 JRNL DOI 10.1021/BI400590H REMARK 2 REMARK 2 RESOLUTION. 1.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : CNS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.68 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.400 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 28646.870 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 81.0 REMARK 3 NUMBER OF REFLECTIONS : 3323 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 SET) : 0.264 REMARK 3 FREE R VALUE : 0.300 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 174 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.023 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.94 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.06 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 54.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 351 REMARK 3 BIN R VALUE (WORKING SET) : 0.3790 REMARK 3 BIN FREE R VALUE : 0.4920 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 15 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.127 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 808 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 93 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 4.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.08000 REMARK 3 B22 (A**2) : 5.95000 REMARK 3 B33 (A**2) : -7.03000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.07000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.32 REMARK 3 ESD FROM SIGMAA (A) : 0.39 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.41 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.380 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.000 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 0.000 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.540 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.160 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.30 REMARK 3 BSOL : 77.86 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : VOTH_TOPOLO REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : VOTH_TOPOLO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 4GQD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000074506. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-OCT-09 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK SI(111) SAGITALLY REMARK 200 FOCUSED MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NOIR-1 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3538 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.940 REMARK 200 RESOLUTION RANGE LOW (A) : 30.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 73.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 54.2 REMARK 200 DATA REDUNDANCY IN SHELL : 1.02 REMARK 200 R MERGE FOR SHELL (I) : 0.22800 REMARK 200 R SYM FOR SHELL (I) : 0.26800 REMARK 200 FOR SHELL : 3.250 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 2ORG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.7MM DNA, 25MM SODIUM CACODYLATE PH REMARK 280 7.0 BUFFER, 10-25MM CALCIUM CHLORIDE, AND 0.8-1.2MM SPERMINE, REMARK 280 EQUILIBRATED AGAINST A RESERVOIR OF 30-40% AQUEOUS MPD., VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 32.84600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 11.78250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 32.84600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 11.78250 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 300 REMARK: THE BIOLOGICAL ASSEMBLY OF THIS STRUCTURE IS THE FOUR REMARK 300 STRANDED DNA HOLLIDAY JUNCTION. DNA HOLLIDAY JUNCTIONS ARE REMARK 300 GENERATED FROM THE TWO STRANDED ASYMMETRIC SUBUNIT THROUGH THE TWO- REMARK 300 FOLD SYMMETRY OPERATOR AT THE CENTER OF THE FOUR-STRANDED JUNCTION. 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: OCTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 BIOMT1 2 -1.000000 0.000000 0.000000 52.37851 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 34.82810 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 212 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 113 LIES ON A SPECIAL POSITION. 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 NA B 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC B 12 O2 REMARK 620 2 HOH B 210 O 148.4 REMARK 620 3 DC D 32 O2 2.3 146.1 REMARK 620 4 HOH D 128 O 77.6 110.2 78.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 102 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 19 OP1 REMARK 620 2 DG D 39 OP1 4.6 REMARK 620 3 HOH D 123 O 140.7 136.2 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ORG RELATED DB: PDB REMARK 900 RELATED ID: 2ORF RELATED DB: PDB REMARK 900 RELATED ID: 3TOK RELATED DB: PDB REMARK 900 RELATED ID: 2ORH RELATED DB: PDB REMARK 900 RELATED ID: 4GRE RELATED DB: PDB REMARK 900 RELATED ID: 4GS2 RELATED DB: PDB REMARK 900 RELATED ID: 4GSG RELATED DB: PDB REMARK 900 RELATED ID: 4GSI RELATED DB: PDB DBREF 4GQD A 1 10 PDB 4GQD 4GQD 1 10 DBREF 4GQD D 31 40 PDB 4GQD 4GQD 31 40 DBREF 4GQD B 11 20 PDB 4GQD 4GQD 11 20 DBREF 4GQD C 21 30 PDB 4GQD 4GQD 21 30 SEQRES 1 A 10 DC DC DG DG DT DA UCL DC DG DG SEQRES 1 B 10 DC DC DG DA DT DA DC DC DG DG SEQRES 1 C 10 DC DC DG DA DT DA DC DC DG DG SEQRES 1 D 10 DC DC DG DG DT DA UCL DC DG DG MODRES 4GQD UCL A 7 DU MODRES 4GQD UCL D 37 DU HET UCL A 7 20 HET UCL D 37 20 HET NA A 101 1 HET NA B 101 1 HET NA B 102 1 HETNAM UCL 5-CHLORO-2'-DEOXYURIDINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM NA SODIUM ION FORMUL 1 UCL 2(C9 H12 CL N2 O8 P) FORMUL 5 NA 3(NA 1+) FORMUL 8 HOH *93(H2 O) LINK O3'A DA A 6 P AUCL A 7 1555 1555 1.61 LINK O3'AUCL A 7 P A DC A 8 1555 1555 1.61 LINK O3'B DA D 36 P BUCL D 37 1555 1555 1.60 LINK O3'BUCL D 37 P B DC D 38 1555 1555 1.60 LINK O2 A DC B 12 NA NA B 101 1555 1555 3.14 LINK OP1A DG B 19 NA NA B 102 1555 1555 2.57 LINK NA NA B 101 O HOH B 210 1555 1555 2.77 LINK NA NA B 101 O2 B DC D 32 1555 1555 3.10 LINK NA NA B 101 O HOH D 128 1555 1555 2.79 LINK NA NA B 102 OP1B DG D 39 1555 1555 2.68 LINK NA NA B 102 O HOH D 123 1555 1555 2.15 SITE 1 AC1 5 DG A 3 DG A 4 DG C 23 DA C 24 SITE 2 AC1 5 HOH C 110 SITE 1 AC2 6 DC B 12 DG B 13 HOH B 210 DC D 32 SITE 2 AC2 6 DG D 33 HOH D 128 SITE 1 AC3 3 DG B 19 DG D 39 HOH D 123 CRYST1 65.692 23.565 37.286 90.00 110.92 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 0.015223 0.000000 0.005819 0.00000 SCALE2 0.000000 0.042436 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028713 0.00000