10 20 30 40 50 60 70 80 1ZEW - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 19-APR-05 1ZEW
TITLE B-DNA
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*TP*CP*TP*AP*GP*AP*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 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 CRYSTALLOGRAPHIC SCREEN, DNA STRUCTURE, HOLLIDAY JUNCTION, KEYWDS 2 MOLECULAR STRUCTURE
EXPDTA X-RAY DIFFRACTION
AUTHOR F.A.HAYS,A.T.TEEGARDEN,Z.J.R.JONES,M.HARMS,D.RAUP,J.WATSON, AUTHOR 2 E.CAVALIERE,P.S.HO
REVDAT 2 24-FEB-09 1ZEW 1 VERSN REVDAT 1 10-MAY-05 1ZEW 0
JRNL AUTH F.A.HAYS,A.TEEGARDEN,Z.J.JONES,M.HARMS,D.RAUP, JRNL AUTH 2 J.WATSON,E.CAVALIERE,P.S.HO JRNL TITL HOW SEQUENCE DEFINES STRUCTURE: A CRYSTALLOGRAPHIC JRNL TITL 2 MAP OF DNA STRUCTURE AND CONFORMATION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 102 7157 2005 JRNL REFN ISSN 0027-8424 JRNL PMID 15870206 JRNL DOI 10.1073/PNAS.0409455102
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.25 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.12 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 49849.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.2 REMARK 3 NUMBER OF REFLECTIONS : 2423 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) : 0.244 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.400 REMARK 3 FREE R VALUE TEST SET COUNT : 228 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.018 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) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.39 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 324 REMARK 3 BIN R VALUE (WORKING SET) : 0.3170 REMARK 3 BIN FREE R VALUE : 0.2760 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 11.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 42 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 : 61 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.02000 REMARK 3 B22 (A**2) : 3.12000 REMARK 3 B33 (A**2) : -2.10000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.81000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.43 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) : 0.57 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 0.90 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.27 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) : 0.067 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 0.105 ; 0.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 0.236 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 0.387 ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 65.24 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: THIS STRUCTURE IS NOT FULLY REFINED. REMARK 3 PART OF A CRYSTALLOGRAPHIC SCREEN - SEE REFERENCE.
REMARK 4 REMARK 4 1ZEW COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-APR-05. REMARK 100 THE RCSB ID CODE IS RCSB032639.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-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) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.127 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3277 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 17.120 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.5500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 51.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.26700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.560 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: NDB ENTRY BD0028 REMARK 200 REMARK 200 REMARK: STRUCTURE IS NOT REFINED TO ITS LOWEST R AND RFREE REMARK 200 VALUES, REFER TO LITERATURE CITATION FOR THIS STRUCTURE.
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NA CACODYLATE, CACL2, SPERMINE, REMARK 280 MPD, IN RESEVOIR,, PH 7.00, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K
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 31.85500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 12.27800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 31.85500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 12.27800 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 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: DIMERIC 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 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 B 21 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 22 LIES ON A SPECIAL POSITION.
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 78 O HOH A 79 1.93 REMARK 500 O5' DT A 5 O HOH A 77 1.98 REMARK 500 O4 DT A 3 O HOH A 44 2.16 REMARK 500 REMARK 500 REMARK: NULL
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 A 35 DISTANCE = 8.58 ANGSTROMS REMARK 525 HOH A 37 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH A 42 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH A 64 DISTANCE = 5.06 ANGSTROMS REMARK 525 HOH A 65 DISTANCE = 5.18 ANGSTROMS REMARK 525 HOH A 72 DISTANCE = 7.49 ANGSTROMS REMARK 525 HOH A 73 DISTANCE = 5.29 ANGSTROMS
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1P4Y RELATED DB: PDB REMARK 900 RELATED ID: 1P4Z RELATED DB: PDB REMARK 900 RELATED ID: 1DCW RELATED DB: PDB REMARK 900 RELATED ID: 1DCV RELATED DB: PDB REMARK 900 RELATED ID: 1ZEX RELATED DB: PDB REMARK 900 RELATED ID: 1ZEY RELATED DB: PDB REMARK 900 RELATED ID: 1ZEZ RELATED DB: PDB REMARK 900 RELATED ID: 1ZF0 RELATED DB: PDB REMARK 900 RELATED ID: 1ZF1 RELATED DB: PDB REMARK 900 RELATED ID: 1ZF2 RELATED DB: PDB REMARK 900 RELATED ID: 1ZF3 RELATED DB: PDB REMARK 900 RELATED ID: 1ZF4 RELATED DB: PDB REMARK 900 RELATED ID: 1ZF5 RELATED DB: PDB REMARK 900 RELATED ID: 1ZF6 RELATED DB: PDB REMARK 900 RELATED ID: 1ZF7 RELATED DB: PDB REMARK 900 RELATED ID: 1ZF8 RELATED DB: PDB REMARK 900 RELATED ID: 1ZF9 RELATED DB: PDB REMARK 900 RELATED ID: 1ZFA RELATED DB: PDB REMARK 900 RELATED ID: 1ZFB RELATED DB: PDB REMARK 900 RELATED ID: 1ZFC RELATED DB: PDB REMARK 900 RELATED ID: 1ZFE RELATED DB: PDB REMARK 900 RELATED ID: 1ZFF RELATED DB: PDB REMARK 900 RELATED ID: 1ZFG RELATED DB: PDB REMARK 900 RELATED ID: 1ZFH RELATED DB: PDB REMARK 900 RELATED ID: 1ZFM RELATED DB: PDB
DBREF 1ZEW A 1 10 PDB 1ZEW 1ZEW 1 10 DBREF 1ZEW B 11 20 PDB 1ZEW 1ZEW 11 20
SEQRES 1 A 10 DC DC DT DC DT DA DG DA DG DG SEQRES 1 B 10 DC DC DT DC DT DA DG DA DG DG
HET NA B 21 1
HETNAM NA SODIUM ION
FORMUL 3 NA NA 1+ FORMUL 4 HOH *61(H2 O)
CRYST1 63.710 24.556 40.631 90.00 122.59 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 0.015696 0.000000 0.010034 0.00000
SCALE2 0.000000 0.040723 0.000000 0.00000
SCALE3 0.000000 0.000000 0.029211 0.00000