HEADER DNA 01-DEC-86 1DN5 TITLE SOLVATION OF THE LEFT-HANDED HEXAMER D(5BRC-G-5BRC-G-5BRC-G) IN TITLE 2 CRYSTALS GROWN AT TWO TEMPERATURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*(CBR)P*GP*(CBR)P*GP*(CBR)P*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS Z-DNA, DOUBLE HELIX, MODIFIED, DNA EXPDTA X-RAY DIFFRACTION AUTHOR B.CHEVRIER,A.C.DOCK,B.HARTMANN,M.LENG,D.MORAS,M.T.THUONG,E.WESTHOF REVDAT 5 07-FEB-24 1DN5 1 LINK REVDAT 4 18-APR-18 1DN5 1 REMARK REVDAT 3 24-JAN-18 1DN5 1 REMARK REVDAT 2 24-FEB-09 1DN5 1 VERSN REVDAT 1 16-APR-87 1DN5 0 JRNL AUTH B.CHEVRIER,A.C.DOCK,B.HARTMANN,M.LENG,D.MORAS,M.T.THUONG, JRNL AUTH 2 E.WESTHOF JRNL TITL SOLVATION OF THE LEFT-HANDED HEXAMER D(5BRC-G-5BRC-G-5 JRNL TITL 2 BRC-G) IN CRYSTALS GROWN AT TWO TEMPERATURES. JRNL REF J.MOL.BIOL. V. 188 707 1986 JRNL REFN ISSN 0022-2836 JRNL PMID 3735433 JRNL DOI 10.1016/S0022-2836(86)80016-X REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NUCLSQ REMARK 3 AUTHORS : WESTHOF,DUMAS,MORAS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 3765 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.125 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 246 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 83 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 SUGAR-BASE BOND DISTANCE (A) : NULL ; NULL REMARK 3 SUGAR-BASE BOND ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 PHOSPHATE BONDS DISTANCE (A) : NULL ; NULL REMARK 3 PHOSPHATE BOND ANGLE, H-BOND (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION CONTACT (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION CONTACT (A) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 SUGAR-BASE BONDS (A**2) : NULL ; NULL REMARK 3 SUGAR-BASE ANGLES (A**2) : NULL ; NULL REMARK 3 PHOSPHATE BONDS (A**2) : NULL ; NULL REMARK 3 PHOSPHATE BOND ANGLE, H-BOND (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DN5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172850. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 310.00 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : ENRAF-NONIUS CAD4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3765 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 18.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION, TEMPERATURE 310.00K, REMARK 280 TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 8.96500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.36500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.41500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.36500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 8.96500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 15.41500 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 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 CBR A 1 O3' DG A 2 P 0.103 REMARK 500 DG A 2 C5 DG A 2 N7 0.038 REMARK 500 DG A 4 O4' DG A 4 C4' -0.087 REMARK 500 DG A 4 C2 DG A 4 N3 0.062 REMARK 500 DG A 4 C6 DG A 4 N1 -0.046 REMARK 500 DG A 6 P DG A 6 O5' 0.081 REMARK 500 DG A 6 C4 DG A 6 C5 -0.048 REMARK 500 DG A 6 C5 DG A 6 N7 0.075 REMARK 500 DG B 8 P DG B 8 OP2 -0.112 REMARK 500 DG B 8 O4' DG B 8 C4' -0.082 REMARK 500 DG B 8 C2 DG B 8 N3 0.056 REMARK 500 DG B 8 C8 DG B 8 N9 -0.045 REMARK 500 DG B 10 P DG B 10 O5' 0.060 REMARK 500 DG B 10 C3' DG B 10 C2' -0.049 REMARK 500 DG B 10 O4' DG B 10 C4' -0.066 REMARK 500 DG B 10 C5 DG B 10 N7 0.040 REMARK 500 DG B 10 N7 DG B 10 C8 -0.055 REMARK 500 DG B 10 N9 DG B 10 C4 0.075 REMARK 500 DG B 10 O3' CBR B 11 P -0.129 REMARK 500 CBR B 11 O3' DG B 12 P 0.083 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 DG A 2 O5' - P - OP1 ANGL. DEV. = -5.8 DEGREES REMARK 500 DG A 2 C6 - N1 - C2 ANGL. DEV. = -4.1 DEGREES REMARK 500 DG A 2 C5 - C6 - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 DG A 4 OP1 - P - OP2 ANGL. DEV. = 11.2 DEGREES REMARK 500 DG A 4 O4' - C1' - C2' ANGL. DEV. = 3.2 DEGREES REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = -4.7 DEGREES REMARK 500 DG A 4 N1 - C2 - N3 ANGL. DEV. = -3.8 DEGREES REMARK 500 DG A 4 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG A 4 C8 - N9 - C1' ANGL. DEV. = -8.2 DEGREES REMARK 500 DG A 6 OP1 - P - OP2 ANGL. DEV. = 11.3 DEGREES REMARK 500 DG A 6 O5' - P - OP2 ANGL. DEV. = -6.5 DEGREES REMARK 500 DG A 6 C6 - N1 - C2 ANGL. DEV. = -4.6 DEGREES REMARK 500 DG A 6 N1 - C2 - N3 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG A 6 C5 - N7 - C8 ANGL. DEV. = -3.0 DEGREES REMARK 500 DG B 8 O5' - P - OP2 ANGL. DEV. = 10.7 DEGREES REMARK 500 DG B 10 OP1 - P - OP2 ANGL. DEV. = 11.7 DEGREES REMARK 500 DG B 10 O5' - P - OP2 ANGL. DEV. = -6.2 DEGREES REMARK 500 DG B 10 O5' - C5' - C4' ANGL. DEV. = -4.9 DEGREES REMARK 500 DG B 10 N1 - C2 - N3 ANGL. DEV. = 4.2 DEGREES REMARK 500 DG B 10 C2 - N3 - C4 ANGL. DEV. = -5.6 DEGREES REMARK 500 DG B 10 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG B 10 N9 - C4 - C5 ANGL. DEV. = -2.7 DEGREES REMARK 500 DG B 10 C3' - O3' - P ANGL. DEV. = 10.4 DEGREES REMARK 500 DG B 12 OP1 - P - OP2 ANGL. DEV. = 11.2 DEGREES REMARK 500 DG B 12 O5' - C5' - C4' ANGL. DEV. = -8.6 DEGREES REMARK 500 DG B 12 N1 - C2 - N2 ANGL. DEV. = 6.1 DEGREES REMARK 500 DG B 12 N3 - C2 - N2 ANGL. DEV. = -4.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 1DN5 A 1 6 PDB 1DN5 1DN5 1 6 DBREF 1DN5 B 7 12 PDB 1DN5 1DN5 7 12 SEQRES 1 A 6 CBR DG CBR DG CBR DG SEQRES 1 B 6 CBR DG CBR DG CBR DG MODRES 1DN5 CBR A 1 DC MODRES 1DN5 CBR A 3 DC MODRES 1DN5 CBR A 5 DC MODRES 1DN5 CBR B 7 DC MODRES 1DN5 CBR B 9 DC MODRES 1DN5 CBR B 11 DC HET CBR A 1 17 HET CBR A 3 20 HET CBR A 5 20 HET CBR B 7 17 HET CBR B 9 20 HET CBR B 11 20 HETNAM CBR 5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE FORMUL 1 CBR 6(C9 H13 BR N3 O7 P) FORMUL 3 HOH *83(H2 O) LINK O3' CBR A 1 P DG A 2 1555 1555 1.71 LINK O3' DG A 2 P CBR A 3 1555 1555 1.67 LINK O3' CBR A 3 P DG A 4 1555 1555 1.65 LINK O3' DG A 4 P CBR A 5 1555 1555 1.59 LINK O3' CBR A 5 P DG A 6 1555 1555 1.58 LINK O3' CBR B 7 P DG B 8 1555 1555 1.62 LINK O3' DG B 8 P CBR B 9 1555 1555 1.59 LINK O3' CBR B 9 P DG B 10 1555 1555 1.56 LINK O3' DG B 10 P CBR B 11 1555 1555 1.48 LINK O3' CBR B 11 P DG B 12 1555 1555 1.69 CRYST1 17.930 30.830 44.730 90.00 90.00 90.00 P 21 21 21 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 0.055772 0.000000 0.000000 0.00000 SCALE2 0.000000 0.032436 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022356 0.00000 HETATM 1 BR CBR A 1 10.866 8.922 -3.024 1.00 10.64 BR HETATM 2 O5' CBR A 1 7.362 12.865 -3.954 1.00 10.45 O HETATM 3 N1 CBR A 1 11.468 12.970 -3.180 1.00 7.71 N HETATM 4 C6 CBR A 1 10.867 11.777 -3.060 1.00 7.54 C HETATM 5 C2 CBR A 1 12.833 13.143 -3.391 1.00 5.16 C HETATM 6 O2 CBR A 1 13.336 14.216 -3.538 1.00 6.54 O HETATM 7 N3 CBR A 1 13.543 11.962 -3.605 1.00 4.03 N HETATM 8 C4 CBR A 1 12.940 10.757 -3.516 1.00 3.88 C HETATM 9 N4 CBR A 1 13.795 9.739 -3.610 1.00 5.90 N HETATM 10 C5 CBR A 1 11.560 10.661 -3.185 1.00 4.63 C HETATM 11 C2' CBR A 1 10.145 14.546 -4.540 1.00 7.86 C HETATM 12 C5' CBR A 1 7.131 13.729 -2.818 1.00 8.70 C HETATM 13 C4' CBR A 1 8.332 14.644 -2.876 1.00 9.87 C HETATM 14 O4' CBR A 1 9.528 14.006 -2.330 1.00 7.20 O HETATM 15 C1' CBR A 1 10.665 14.173 -3.167 1.00 7.11 C HETATM 16 C3' CBR A 1 8.863 15.316 -4.133 1.00 5.69 C HETATM 17 O3' CBR A 1 9.347 16.639 -3.784 1.00 12.37 O