HEADER DNA 02-FEB-07 2ORF TITLE DIRECTING MACROMOLECULAR CONFORMATION THROUGH HALOGEN BONDS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*CP*GP*GP*TP*AP*(BRU)P*CP*GP*G)-3'); COMPND 3 CHAIN: A; 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; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHETICALLY PREPARED DECANUCLEOTIDE SEQUENCES.; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES KEYWDS DNA HOLLIDAY JUNCTION, HALOGEN BOND, DNA EXPDTA X-RAY DIFFRACTION AUTHOR A.R.VOTH,F.A.HAYS,P.S.HO REVDAT 5 30-AUG-23 2ORF 1 REMARK LINK REVDAT 4 18-OCT-17 2ORF 1 REMARK REVDAT 3 24-FEB-09 2ORF 1 VERSN REVDAT 2 15-MAY-07 2ORF 1 JRNL REVDAT 1 27-MAR-07 2ORF 0 JRNL AUTH A.R.VOTH,F.A.HAYS,P.S.HO JRNL TITL DIRECTING MACROMOLECULAR CONFORMATION THROUGH HALOGEN BONDS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 104 6188 2007 JRNL REFN ISSN 0027-8424 JRNL PMID 17379665 JRNL DOI 10.1073/PNAS.0610531104 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 62751.600 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 87.6 REMARK 3 NUMBER OF REFLECTIONS : 4247 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) : 0.223 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.400 REMARK 3 FREE R VALUE TEST SET COUNT : 441 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.012 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 62.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 432 REMARK 3 BIN R VALUE (WORKING SET) : 0.3020 REMARK 3 BIN FREE R VALUE : 0.3420 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 12.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 63 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.043 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 404 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 101 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.23000 REMARK 3 B22 (A**2) : 7.27000 REMARK 3 B33 (A**2) : -6.05000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.48000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.28 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) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.35 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.870 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 139.4 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 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.LINK REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2ORF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-FEB-07. REMARK 100 THE DEPOSITION ID IS D_1000041492. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JAN-05 REMARK 200 TEMPERATURE (KELVIN) : 133 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4350 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 20.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.7 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.03200 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) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 61.7 REMARK 200 DATA REDUNDANCY IN SHELL : 1.80 REMARK 200 R MERGE FOR SHELL (I) : 0.09300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: 1P54 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25 MM SODIUM CACODYLATE, 10 MM CALCIUM REMARK 280 CHLORIDE, 1.0 MM SPERMINE, AND 0.35 MM OF EACH DNA STRAND., PH REMARK 280 7.0, VAPOR 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 32.94500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 12.10350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 32.94500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 12.10350 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 SECOND HALF OF THE BIOLOGICAL ASSEMBLY (THE HOLLIDAY REMARK 300 JUNCTION) IS GENERATED BY THE TWO FOLD ROTATION: -X, Y, -Z+1 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 -13.37713 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 34.81228 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 83 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 28 LIES ON A SPECIAL POSITION. 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 B 17 N3 DC B 17 C4 0.046 REMARK 500 REMARK 500 REMARK: NULL 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 DT A 5 N1 - C1' - C2' ANGL. DEV. = 8.4 DEGREES REMARK 500 DC B 17 C2 - N3 - C4 ANGL. DEV. = 7.0 DEGREES REMARK 500 DC B 17 N3 - C4 - C5 ANGL. DEV. = -7.4 DEGREES REMARK 500 DC B 17 N1 - C2 - O2 ANGL. DEV. = 3.8 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 NA B 25 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 21 O REMARK 620 2 HOH B 24 O 117.3 REMARK 620 3 HOH B 60 O 149.7 63.9 REMARK 620 4 HOH B 69 O 56.4 85.1 95.0 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 NA B 25 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ORG RELATED DB: PDB REMARK 900 RELATED ID: 2ORH RELATED DB: PDB DBREF 2ORF A 1 10 PDB 2ORF 2ORF 1 10 DBREF 2ORF B 11 20 PDB 2ORF 2ORF 11 20 SEQRES 1 A 10 DC DC DG DG DT DA BRU DC DG DG SEQRES 1 B 10 DC DC DG DA DT DA DC DC DG DG MODRES 2ORF BRU A 7 DU HET BRU A 7 20 HET NA B 25 1 HETNAM BRU 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE HETNAM NA SODIUM ION FORMUL 1 BRU C9 H12 BR N2 O8 P FORMUL 3 NA NA 1+ FORMUL 4 HOH *101(H2 O) LINK O3' DA A 6 P BRU A 7 1555 1555 1.61 LINK O3' BRU A 7 P DC A 8 1555 1555 1.60 LINK O HOH B 21 NA NA B 25 1555 1555 2.65 LINK O HOH B 24 NA NA B 25 1555 1555 2.33 LINK NA NA B 25 O HOH B 60 1555 1555 2.14 LINK NA NA B 25 O HOH B 69 1555 1555 2.76 SITE 1 AC1 4 HOH B 21 HOH B 24 HOH B 60 HOH B 69 CRYST1 65.890 24.207 37.294 90.00 111.02 90.00 C 1 2 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 0.015177 0.000000 0.005832 0.00000 SCALE2 0.000000 0.041310 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028725 0.00000