HEADER DNA 04-MAR-99 455D TITLE A6/A18 INTER-STRAND DITHIOBIS(PROPANE)-CROSSLINKED DODECAMER TITLE 2 (CGCGAATTCGCG)2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*CP*GP*AP*(SSP)AP*TP*TP*CP*GP*CP*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: COMPLEXED WITH THIOPROPANE SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS INTER-STRAND CROSSLINKING, DODECAMER CGCGAATTCGCG/CGCGAATTCGCG, KEYWDS 2 DEOXYRIBONUCLEIC ACID, DNA EXPDTA X-RAY DIFFRACTION AUTHOR T.K.CHIU,M.KACZOR-GRZESKOWIAK,R.E.DICKERSON REVDAT 5 03-APR-24 455D 1 REMARK REVDAT 4 28-FEB-24 455D 1 REMARK LINK REVDAT 3 29-MAY-19 455D 1 REMARK LINK REVDAT 2 24-FEB-09 455D 1 VERSN REVDAT 1 08-OCT-99 455D 0 JRNL AUTH T.K.CHIU,M.KACZOR-GRZESKOWIAK,R.E.DICKERSON JRNL TITL ABSENCE OF MINOR GROOVE MONOVALENT CATIONS IN THE JRNL TITL 2 CROSSLINKED DODECAMER C-G-C-G-A-A-T-T-C-G-C-G. JRNL REF J.MOL.BIOL. V. 292 589 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10497024 JRNL DOI 10.1006/JMBI.1999.3075 REMARK 2 REMARK 2 RESOLUTION. 1.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.843 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 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) (%) : 88.5 REMARK 3 NUMBER OF REFLECTIONS : 11016 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) : 0.208 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1055 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 486 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.85 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.56 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.65000 REMARK 3 B22 (A**2) : -3.12000 REMARK 3 B33 (A**2) : -1.40000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.65 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.460 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 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: STARTING MODEL IS IDEAL B-DNA RMS REMARK 3 -FITTED ONTO COORDINATES OF ORIGINAL DREW STRUCTURE (1BNA) REMARK 4 REMARK 4 455D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000179237. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL 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 : MIRRORS 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 : 11200 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.430 REMARK 200 RESOLUTION RANGE LOW (A) : 8.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.4 REMARK 200 DATA REDUNDANCY : 9.490 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 38.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.73 REMARK 200 R MERGE FOR SHELL (I) : 0.15600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 10.90 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMEN REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: IDEAL B-DNA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K 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 12.27200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.48200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.65150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.48200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.27200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.65150 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: 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 N6 DA B 18 CA2 SSP A 27 1.45 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 41 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH A 89 DISTANCE = 6.29 ANGSTROMS REMARK 525 HOH A 94 DISTANCE = 6.31 ANGSTROMS REMARK 525 HOH A 155 DISTANCE = 7.59 ANGSTROMS REMARK 525 HOH A 156 DISTANCE = 6.51 ANGSTROMS REMARK 525 HOH B 120 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH B 139 DISTANCE = 6.50 ANGSTROMS REMARK 525 HOH B 161 DISTANCE = 6.28 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 MG A 25 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 167 O REMARK 620 2 HOH A 168 O 176.1 REMARK 620 3 HOH A 169 O 90.4 93.5 REMARK 620 4 HOH A 171 O 89.9 90.2 87.4 REMARK 620 5 HOH B 170 O 89.6 86.5 176.8 95.8 REMARK 620 6 HOH B 172 O 92.4 87.7 88.3 175.1 88.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 26 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 173 O REMARK 620 2 HOH A 174 O 169.0 REMARK 620 3 HOH A 175 O 93.1 81.6 REMARK 620 4 HOH A 176 O 88.1 97.4 178.5 REMARK 620 5 HOH A 177 O 84.4 86.2 92.4 88.7 REMARK 620 6 HOH A 178 O 91.2 98.3 89.2 89.9 175.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 27 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA B 17 OP1 REMARK 620 2 HOH B 179 O 93.5 REMARK 620 3 HOH B 180 O 86.3 169.7 REMARK 620 4 HOH B 182 O 81.8 95.6 94.6 REMARK 620 5 HOH B 183 O 98.5 85.1 84.7 179.3 REMARK 620 6 HOH B 184 O 168.5 92.7 89.5 88.0 91.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 25 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 26 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 27 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SSP A 27 DBREF 455D A 1 12 PDB 455D 455D 1 12 DBREF 455D B 13 24 PDB 455D 455D 13 24 SEQRES 1 A 12 DC DG DC DG DA DA DT DT DC DG DC DG SEQRES 1 B 12 DC DG DC DG DA DA DT DT DC DG DC DG HET MG A 25 1 HET MG A 26 1 HET SSP A 27 8 HET MG B 27 1 HETNAM MG MAGNESIUM ION HETNAM SSP DITHIOBIS-(PROPANE) FORMUL 3 MG 3(MG 2+) FORMUL 5 SSP C6 H14 S2 FORMUL 7 HOH *150(H2 O) LINK N6 DA A 6 CA1 SSP A 27 1555 1555 1.45 LINK MG MG A 25 O HOH A 167 1555 1555 2.09 LINK MG MG A 25 O HOH A 168 1555 1555 2.06 LINK MG MG A 25 O HOH A 169 1555 1555 2.08 LINK MG MG A 25 O HOH A 171 1555 1555 2.01 LINK MG MG A 25 O HOH B 170 1555 1555 2.07 LINK MG MG A 25 O HOH B 172 1555 1555 2.04 LINK MG MG A 26 O HOH A 173 1555 1555 2.15 LINK MG MG A 26 O HOH A 174 1555 1555 2.03 LINK MG MG A 26 O HOH A 175 1555 1555 2.01 LINK MG MG A 26 O HOH A 176 1555 1555 2.08 LINK MG MG A 26 O HOH A 177 1555 1555 2.04 LINK MG MG A 26 O HOH A 178 1555 1555 1.97 LINK OP1 DA B 17 MG MG B 27 1555 1555 2.21 LINK MG MG B 27 O HOH B 179 1555 1555 2.02 LINK MG MG B 27 O HOH B 180 1555 1555 2.08 LINK MG MG B 27 O HOH B 182 1555 1555 2.12 LINK MG MG B 27 O HOH B 183 1555 1555 1.98 LINK MG MG B 27 O HOH B 184 1555 1555 2.05 SITE 1 AC1 6 HOH A 167 HOH A 168 HOH A 169 HOH A 171 SITE 2 AC1 6 HOH B 170 HOH B 172 SITE 1 AC2 6 HOH A 173 HOH A 174 HOH A 175 HOH A 176 SITE 2 AC2 6 HOH A 177 HOH A 178 SITE 1 AC3 6 DA B 17 HOH B 179 HOH B 180 HOH B 182 SITE 2 AC3 6 HOH B 183 HOH B 184 SITE 1 AC4 6 DA A 5 DA A 6 DT A 7 DA B 17 SITE 2 AC4 6 DA B 18 DT B 19 CRYST1 24.544 39.303 66.964 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 0.040743 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025443 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014933 0.00000