HEADER DNA 25-APR-03 1P54 TITLE EFFECT OF SEQUENCE ON THE CONFORMATIONAL GEOMETRY OF DNA HOLLIDAY TITLE 2 JUNCTIONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*AP*GP*TP*AP*CP*(BRU)P*GP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: DNA WAS SYNTHESIZED ON AN APPLIED BIOSYSTEMS DNA SOURCE 4 SYNTHESIZER USING PHOSPHORAMIDITE CHEMISTRY, WITH THE TRITYL- SOURCE 5 PROTECTING GROUP LEFT INTACT AT THE 5-TERMINAL NUCLEOTIDE, FOR SOURCE 6 SUBSEQUENT HPLC PURIFICATION, THEN DEPROTECTED BY TREATMENT WITH 3% SOURCE 7 ACETIC ACID FOR FIFTEEN MINUTES, NEUTRALIZED WITH AMMONIUM SOURCE 8 HYDROXIDE, AND DESALTED ON A SIGMA G-25 SEPHADEX COLUMN. KEYWDS DNA HOLLIDAY JUNCTION, FOUR-WAY JUNCTION, STACKED-X JUNCTION, KEYWDS 2 BROMINATED URACIL, DNA EXPDTA X-RAY DIFFRACTION AUTHOR F.A.HAYS,J.M.VARGASON,P.S.HO REVDAT 4 16-AUG-23 1P54 1 REMARK LINK REVDAT 3 16-NOV-11 1P54 1 VERSN HETATM REVDAT 2 24-FEB-09 1P54 1 VERSN REVDAT 1 02-SEP-03 1P54 0 JRNL AUTH F.A.HAYS,J.M.VARGASON,P.S.HO JRNL TITL EFFECT OF SEQUENCE ON THE CONFORMATION OF DNA HOLLIDAY JRNL TITL 2 JUNCTIONS JRNL REF BIOCHEMISTRY V. 42 9586 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 12911300 JRNL DOI 10.1021/BI0346603 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.18 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 86.7 REMARK 3 NUMBER OF REFLECTIONS : 3745 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) : 0.215 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.400 REMARK 3 FREE R VALUE TEST SET COUNT : 388 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 60.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 385 REMARK 3 BIN R VALUE (WORKING SET) : 0.2590 REMARK 3 BIN FREE R VALUE : 0.2480 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 37 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.041 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 : 2 REMARK 3 SOLVENT ATOMS : 87 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 4.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.14 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) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 0.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.370 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 : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1P54 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-APR-03. REMARK 100 THE DEPOSITION ID IS D_1000019018. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-DEC-02 REMARK 200 TEMPERATURE (KELVIN) : 103.0 REMARK 200 PH : 7.50 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.542 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4177 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 19.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 82.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 4.0500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 34.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.18900 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: EPMR REMARK 200 STARTING MODEL: 1L6B USED FOR INITIAL SOLUTION VIA MOLECULAR REMARK 200 REPLACEMENT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.6MM DNA, 5MM TRIS-HCL, 120MM CALCIUM REMARK 280 ACETATE, 16% 2-METHYL-2,4-PENTANE DIOL, PH 7.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 298K, PH 7.50 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 32.42000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 11.29000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 32.42000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 11.29000 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: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF TWO CHAINS A AND B. THE FULL FOUR STRANDED REMARK 300 HOLLIDAY JUNCTION STRUCTURE CAN BE GENERATED BY THE FOLLOWING: REMARK 300 MATRIX = (-1.00000 0.00001 0.00000) (0.00001 1.00000 -0.00002) REMARK 300 (0.00000 -0.00002 -1.00000) TRANSLATION = (0.00022 0.00018 -0.00034) 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 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 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 NA NA A 37 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 68 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 86 LIES ON A SPECIAL POSITION. 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 B 19 0.05 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 67 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 27 O REMARK 620 2 HOH A 80 O 83.5 REMARK 620 3 HOH A 81 O 106.8 76.9 REMARK 620 4 HOH A 82 O 71.0 152.0 121.1 REMARK 620 5 HOH B 69 O 136.1 140.0 84.5 67.1 REMARK 620 6 HOH B 75 O 90.3 97.6 161.0 71.7 88.8 REMARK 620 7 HOH B 93 O 150.1 89.4 99.7 106.7 59.1 61.8 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 NA A 37 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 67 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1P4Y RELATED DB: PDB REMARK 900 EFFECT OF SEQUENCE ON THE CONFORMATIONAL GEOMETRY OF DNA HOLLIDAY REMARK 900 JUNCTIONS REMARK 900 RELATED ID: 1P4Z RELATED DB: PDB REMARK 900 EFFECT OF SEQUENCE ON THE CONFORMATIONAL GEOMETRY OF DNA HOLLIDAY REMARK 900 JUNCTIONS DBREF 1P54 A 1 10 PDB 1P54 1P54 1 10 DBREF 1P54 B 11 20 PDB 1P54 1P54 11 20 SEQRES 1 A 10 DC DC DA DG DT DA DC BRU DG DG SEQRES 1 B 10 DC DC DA DG DT DA DC BRU DG DG MODRES 1P54 BRU A 8 DU MODRES 1P54 BRU B 18 DU HET BRU A 8 20 HET BRU B 18 20 HET NA A 37 1 HET CA A 67 1 HETNAM BRU 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE HETNAM NA SODIUM ION HETNAM CA CALCIUM ION FORMUL 1 BRU 2(C9 H12 BR N2 O8 P) FORMUL 3 NA NA 1+ FORMUL 4 CA CA 2+ FORMUL 5 HOH *87(H2 O) LINK O3' DC A 7 P BRU A 8 1555 1555 1.61 LINK O3' BRU A 8 P DG A 9 1555 1555 1.61 LINK O3' DC B 17 P BRU B 18 1555 1555 1.61 LINK O3' BRU B 18 P DG B 19 1555 1555 1.61 LINK OP2 DA A 6 NA NA A 37 1555 1555 2.78 LINK O HOH A 27 CA CA A 67 1555 1555 2.30 LINK CA CA A 67 O HOH A 80 1555 1555 2.28 LINK CA CA A 67 O HOH A 81 1555 1555 2.24 LINK CA CA A 67 O HOH A 82 1555 1555 2.95 LINK CA CA A 67 O HOH B 69 1555 2555 3.12 LINK CA CA A 67 O HOH B 75 1555 2555 3.01 LINK CA CA A 67 O HOH B 93 1555 2555 3.26 SITE 1 AC1 1 DA A 6 SITE 1 AC2 5 HOH A 27 HOH A 80 HOH A 81 HOH A 82 SITE 2 AC2 5 HOH B 75 CRYST1 64.840 22.580 38.070 90.00 106.78 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 0.015423 0.000000 0.004649 0.00000 SCALE2 0.000000 0.044293 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027436 0.00000