PDB Short entry for 1CW9 HEADER DNA 26-AUG-99 1CW9 TITLE DNA DECAMER WITH AN ENGINEERED CROSSLINK IN THE MINOR GROOVE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*AP*GP*(G47)P*CP*CP*TP*GP*G)-3'; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CROSSLINKED DNA WAS SYNTHESIZED BY THE CONVERTIBLE SOURCE 4 NUCLEOSIDE APPROACH KEYWDS CROSSLINKED DOUBLE-HELICAL DNA, BASE-PAIR OPENING, PARTIAL BASE KEYWDS 2 FLIPPING., DNA EXPDTA X-RAY DIFFRACTION AUTHOR D.M.F.VAN AALTEN,D.A.ERLANSON,G.L.VERDINE,L.JOSHUA-TOR REVDAT 7 04-OCT-17 1CW9 1 REMARK REVDAT 6 01-FEB-17 1CW9 1 AUTHOR VERSN REVDAT 5 24-FEB-09 1CW9 1 VERSN REVDAT 4 01-APR-03 1CW9 1 JRNL REVDAT 3 28-JUN-02 1CW9 1 REMARK REVDAT 2 27-NOV-00 1CW9 5 REVDAT 1 14-OCT-99 1CW9 0 JRNL AUTH D.M.VAN AALTEN,D.A.ERLANSON,G.L.VERDINE,L.JOSHUA-TOR JRNL TITL A STRUCTURAL SNAPSHOT OF BASE-PAIR OPENING IN DNA. JRNL REF PROC.NATL.ACAD.SCI.USA V. 96 11809 1999 JRNL REFN ISSN 0027-8424 JRNL PMID 10518532 JRNL DOI 10.1073/PNAS.96.21.11809 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 : CNS NUCLEIC ACID PARAMETERS USING SOFT VAN REMARK 3 DER WAALS PARAMETERS (PARKINSON ET AL., ACTA REMARK 3 D, 52, 57-64 (1996)). REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.00 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) (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 15525 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) : 0.203 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 782 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) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.61 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.00 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 (%) : 5.00 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 : 820 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 271 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.89500 REMARK 3 B22 (A**2) : -2.35800 REMARK 3 B33 (A**2) : -1.53700 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) : 1.530 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED CNS REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 3.938 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.824 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 2.875 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.828 ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT - CNS CALCULATED MASK 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 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: MAXIMUM LIKELIHOOD. REMARK 4 REMARK 4 1CW9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-SEP-99. REMARK 100 THE DEPOSITION ID IS D_1000009586. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAR-98 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X26C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0800 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62990 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 13.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.32000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: BDJ017 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, CALCIUM CHLORIDE, SODIUM REMARK 280 CHLORIDE, SPERMINE TETRACHLORIDE, SODIUM CACODYLATE, PH 7.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, 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 17.21750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.20600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.59000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.20600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.21750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.59000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O5' DC A 1 OP1 DC B 6 4456 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 DC A 2 0.07 SIDE CHAIN REMARK 500 DA A 3 0.06 SIDE CHAIN REMARK 500 DC A 7 0.07 SIDE CHAIN REMARK 500 DG A 9 0.10 SIDE CHAIN REMARK 500 DA B 3 0.05 SIDE CHAIN REMARK 500 DC B 6 0.06 SIDE CHAIN REMARK 500 DC B 7 0.09 SIDE CHAIN REMARK 500 DA C 3 0.07 SIDE CHAIN REMARK 500 DC C 7 0.10 SIDE CHAIN REMARK 500 DG C 9 0.06 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 11 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G47 A 5 O6 REMARK 620 2 G47 B 5 O6 72.1 REMARK 620 3 HOH A 16 O 78.1 123.2 REMARK 620 4 HOH A 21 O 122.2 76.3 80.8 REMARK 620 5 HOH A 30 O 142.8 145.0 78.3 81.3 REMARK 620 6 HOH A 26 O 73.4 119.9 95.0 161.9 80.6 REMARK 620 7 HOH B 359 O 119.2 78.5 157.1 99.7 79.2 77.5 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 CA A 11 DBREF 1CW9 A 1 10 PDB 1CW9 1CW9 1 10 DBREF 1CW9 B 1 10 PDB 1CW9 1CW9 1 10 DBREF 1CW9 C 1 10 PDB 1CW9 1CW9 1 10 DBREF 1CW9 D 1 10 PDB 1CW9 1CW9 1 10 SEQRES 1 A 10 DC DC DA DG G47 DC DC DT DG DG SEQRES 1 B 10 DC DC DA DG G47 DC DC DT DG DG SEQRES 1 C 10 DC DC DA DG G47 DC DC DT DG DG SEQRES 1 D 10 DC DC DA DG G47 DC DC DT DG DG MODRES 1CW9 G47 A 5 DG MODRES 1CW9 G47 B 5 DG MODRES 1CW9 G47 C 5 DG MODRES 1CW9 G47 D 5 DG HET G47 A 5 25 HET G47 B 5 25 HET G47 C 5 25 HET G47 D 5 25 HET CA A 11 1 HETNAM G47 N2-ETHANETHIOL-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM CA CALCIUM ION FORMUL 1 G47 4(C12 H18 N5 O7 P S) FORMUL 5 CA CA 2+ FORMUL 6 HOH *271(H2 O) LINK SG G47 A 5 SG G47 B 5 1555 1555 2.09 LINK SG G47 C 5 SG G47 D 5 1555 1555 2.15 LINK O6 G47 A 5 CA CA A 11 1555 1555 2.51 LINK O6 G47 B 5 CA CA A 11 1555 1555 2.54 LINK CA CA A 11 O HOH A 16 1555 1555 2.44 LINK CA CA A 11 O HOH A 21 1555 1555 2.32 LINK CA CA A 11 O HOH A 30 1555 1555 2.49 LINK CA CA A 11 O HOH A 26 1555 1555 2.37 LINK CA CA A 11 O HOH B 359 1555 1555 2.41 LINK O3' DG A 4 P G47 A 5 1555 1555 1.60 LINK O3' G47 A 5 P DC A 6 1555 1555 1.60 LINK O3' DG B 4 P G47 B 5 1555 1555 1.61 LINK O3' G47 B 5 P DC B 6 1555 1555 1.61 LINK O3' DG C 4 P G47 C 5 1555 1555 1.60 LINK O3' G47 C 5 P DC C 6 1555 1555 1.60 LINK O3' DG D 4 P G47 D 5 1555 1555 1.61 LINK O3' G47 D 5 P DC D 6 1555 1555 1.59 SITE 1 AC1 7 G47 A 5 HOH A 16 HOH A 21 HOH A 26 SITE 2 AC1 7 HOH A 30 G47 B 5 HOH B 359 CRYST1 34.435 43.180 72.412 90.00 90.00 90.00 P 21 21 21 16 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 0.029040 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023159 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013810 0.00000