10 20 30 40 50 60 70 80 1P4Y - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 24-APR-03 1P4Y
TITLE EFFECT OF SEQUENCE ON THE CONFORMATIONAL GEOMETRY OF DNA TITLE 2 HOLLIDAY JUNCTIONS
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*GP*GP*CP*GP*CP*CP*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 SOURCE 4 BIOSYSTEMS DNA SYNTHESIZER USING PHOSPHORAMIDITE CHEMISTRY, SOURCE 5 WITH THE TRITYL-PROTECTING GROUP LEFT INTACT AT THE 5- SOURCE 6 TERMINAL NUCLEOTIDE, FOR SUBSEQUENT HPLC PURIFICATION, SOURCE 7 THEN DEPROTECTED BY TREATMENT WITH 3% ACETIC ACID FOR SOURCE 8 FIFTEEN MINUTES, NEUTRALIZED WITH AMMONIUM HYDROXIDE, AND SOURCE 9 DESALTED ON A SIGMA G-25 SEPHADEX COLUMN.
KEYWDS HOLLIDAY JUNCTION, DNA FOUR-WAY JUNCTION
EXPDTA X-RAY DIFFRACTION
AUTHOR F.A.HAYS,J.M.VARGASON,P.S.HO
REVDAT 2 24-FEB-09 1P4Y 1 VERSN REVDAT 1 02-SEP-03 1P4Y 0
JRNL AUTH F.A.HAYS,J.M.VARGASON,P.S.HO JRNL TITL EFFECT OF SEQUENCE ON THE CONFORMATION OF DNA JRNL TITL 2 HOLLIDAY JUNCTIONS JRNL REF BIOCHEMISTRY V. 42 9586 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 12911300 JRNL DOI 10.1021/BI0346603
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 77.1 REMARK 3 NUMBER OF REFLECTIONS : 4436 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) : 0.229 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 490 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 40.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 374 REMARK 3 BIN R VALUE (WORKING SET) : 0.2090 REMARK 3 BIN FREE R VALUE : 0.2850 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 39 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.046 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 : 4 REMARK 3 SOLVENT ATOMS : 108 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 1.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.70 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) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.03 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) : 0.10 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.20 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.57 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 1P4Y COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-APR-03. REMARK 100 THE RCSB ID CODE IS RCSB019012.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JAN-03 REMARK 200 TEMPERATURE (KELVIN) : 103.0 REMARK 200 PH : 7.00 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 : 4940 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 22.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 74.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 21.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.27900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.140 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: UD0008 REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5MM DNA, 25MM SODIUM CACODYLATE, REMARK 280 7.5MM CACL2, 0.1MM SPERMINE TETRAHYDROCHLORIDE, PH 7.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K, PH 7.00
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 33.25650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 12.08950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 33.25650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 12.08950 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 -0.00046 -0.00015 ) (-0.00046 1.00000 0.00072 REMARK 300 ) (0.00015 0.00072 -1.00000 ) TRANSLATION= (-12.65734 -0.02663 REMARK 300 34.77174)
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 -12.66218 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 34.77018
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 30 DISTANCE = 7.33 ANGSTROMS REMARK 525 HOH B 91 DISTANCE = 8.02 ANGSTROMS
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 A 21 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 25 O REMARK 620 2 HOH A 109 O 143.1 REMARK 620 3 HOH A 24 O 77.2 134.8 REMARK 620 4 HOH A 56 O 147.8 66.6 83.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 36 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC A 1 O5' REMARK 620 2 HOH A 82 O 121.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 49 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 56 O REMARK 620 2 DG A 10 N3 101.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 55 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 19 O4' REMARK 620 2 HOH B 75 O 57.0 REMARK 620 N 1
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 21 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 36 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 49 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 55
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1P4Z RELATED DB: PDB REMARK 900 EFFECT OF SEQUENCE ON THE CONFORMATIONAL GEOMETRY OF DNA REMARK 900 HOLLIDAY JUNCTIONS REMARK 900 RELATED ID: 1P54 RELATED DB: PDB REMARK 900 EFFECT OF SEQUENCE ON THE CONFORMATIONAL GEOMETRY OF DNA REMARK 900 HOLLIDAY JUNCTIONS
DBREF 1P4Y A 1 10 PDB 1P4Y 1P4Y 1 10 DBREF 1P4Y B 11 20 PDB 1P4Y 1P4Y 11 20
SEQRES 1 A 10 DC DC DG DG DC DG DC DC DG DG SEQRES 1 B 10 DC DC DG DG DC DG DC DC DG DG
HET NA A 21 1 HET NA A 36 1 HET NA A 49 1 HET NA B 55 1
HETNAM NA SODIUM ION
FORMUL 3 NA 4(NA 1+) FORMUL 7 HOH *108(H2 O)
LINK NA NA A 21 O HOH A 25 1555 1555 2.47 LINK NA NA A 21 O HOH A 109 1555 1555 2.48 LINK NA NA A 36 O5' DC A 1 1555 1555 2.48 LINK NA NA A 49 O HOH A 56 1555 1555 2.56 LINK N3 DG A 10 NA NA A 49 1555 1555 2.95 LINK O4' DG B 19 NA NA B 55 1555 1555 2.63 LINK NA NA A 21 O HOH A 24 1555 1555 2.81 LINK NA NA A 21 O HOH A 56 1555 1555 2.72 LINK NA NA A 36 O HOH A 82 1555 1555 2.64 LINK NA NA B 55 O HOH B 75 1555 1555 2.81
SITE 1 AC1 6 HOH A 24 HOH A 25 NA A 49 HOH A 56 SITE 2 AC1 6 HOH A 109 HOH B 76 SITE 1 AC2 4 DC A 1 DC A 2 HOH A 82 DG B 14 SITE 1 AC3 3 DG A 10 NA A 21 HOH A 56 SITE 1 AC4 2 DG B 19 HOH B 75
CRYST1 66.513 24.179 37.004 90.00 110.01 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 0.015035 0.000000 0.005475 0.00000
SCALE2 0.000000 0.041358 0.000000 0.00000
SCALE3 0.000000 0.000000 0.028760 0.00000