HEADER DNA 19-AUG-14 4R48 TITLE RACEMIC CRYSTAL STRUCTURE OF A CALCIUM-BOUND DNA FOUR-WAY JUNCTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: DNA FOUR-WAY JUNCTION SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS RACEMIC DNA, RACEMATES, DNA EXPDTA X-RAY DIFFRACTION AUTHOR P.K.MANDAL,G.W.COLLIE,B.KAUFFMANN,I.HUC REVDAT 4 20-SEP-23 4R48 1 LINK REVDAT 3 28-AUG-19 4R48 1 REMARK REVDAT 2 14-JAN-15 4R48 1 JRNL REVDAT 1 12-NOV-14 4R48 0 JRNL AUTH P.K.MANDAL,G.W.COLLIE,B.KAUFFMANN,I.HUC JRNL TITL RACEMIC DNA CRYSTALLOGRAPHY. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 53 14424 2014 JRNL REFN ISSN 1433-7851 JRNL PMID 25358289 JRNL DOI 10.1002/ANIE.201409014 REMARK 2 REMARK 2 RESOLUTION. 2.33 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 4142 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.289 REMARK 3 R VALUE (WORKING SET) : 0.286 REMARK 3 FREE R VALUE : 0.341 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.260 REMARK 3 FREE R VALUE TEST SET COUNT : 218 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 32.9136 - 2.9349 0.99 1966 115 0.2468 0.2969 REMARK 3 2 2.9349 - 2.3300 0.99 1958 103 0.4543 0.5694 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.520 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.84 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.59 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 452 REMARK 3 ANGLE : 1.066 694 REMARK 3 CHIRALITY : 0.050 78 REMARK 3 PLANARITY : 0.009 20 REMARK 3 DIHEDRAL : 37.048 192 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A REMARK 3 SELECTION : CHAIN B REMARK 3 ATOM PAIRS NUMBER : 192 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4R48 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000086878. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUN-14 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 : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9998 REMARK 200 MONOCHROMATOR : SI(111) CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4156 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.330 REMARK 200 RESOLUTION RANGE LOW (A) : 32.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.04420 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.5500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.29290 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.680 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1DCW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 MM DNA, 75 MM SODIUM CACODYLATE, 30 REMARK 280 MM CALCIUM CHLORIDE, 1 MM SPERMINE, 35% MPD, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2/c 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z+1/2 REMARK 290 3555 -X,-Y,-Z REMARK 290 4555 X,-Y,Z+1/2 REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 7555 -X+1/2,-Y+1/2,-Z REMARK 290 8555 X+1/2,-Y+1/2,Z+1/2 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 -15.67641 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 32.91061 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 -15.67641 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 32.91061 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 32.97500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 11.67750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 17.29859 REMARK 290 SMTRY2 6 0.000000 1.000000 0.000000 11.67750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 32.91061 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 32.97500 REMARK 290 SMTRY2 7 0.000000 -1.000000 0.000000 11.67750 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 17.29859 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 11.67750 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 32.91061 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: ONE CROSSING STRAND AND ONE NON-CROSSING STRAND FORM A REMARK 300 CONTINUOUS NETWORK IN THE CRYSTAL. 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 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 -15.67641 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 32.91061 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 HOH A 202 LIES ON A SPECIAL POSITION. 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 DG A 3 O3' DG A 3 C3' -0.039 REMARK 500 DC B 17 O3' DC B 17 C3' -0.047 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 NA A 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 201 O REMARK 620 2 HOH A 204 O 65.1 REMARK 620 3 HOH A 206 O 77.8 74.5 REMARK 620 4 HOH B 203 O 121.1 140.1 69.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 101 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 201 O REMARK 620 2 HOH B 202 O 70.0 REMARK 620 3 HOH B 204 O 144.4 75.0 REMARK 620 4 HOH B 205 O 93.1 70.7 81.4 REMARK 620 5 HOH B 206 O 67.0 111.4 122.2 156.3 REMARK 620 6 HOH B 207 O 75.5 131.0 135.9 77.7 84.6 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4R44 RELATED DB: PDB REMARK 900 RACEMIC CRYSTAL STRUCTURE OF A TETRAMOLECULAR DNA G-QUADRUPLEX REMARK 900 RELATED ID: 4R45 RELATED DB: PDB REMARK 900 RACEMIC CRYSTAL STRUCTURE OF A BIMOLECULAR DNA G-QUADRUPLEX (P-1) REMARK 900 RELATED ID: 4R47 RELATED DB: PDB REMARK 900 RACEMIC CRYSTAL STRUCTURE OF A BIMOLECULAR DNA G-QUADRUPLEX (P21/N) REMARK 900 RELATED ID: 4R49 RELATED DB: PDB REMARK 900 RACEMIC CRYSTAL STRUCTURE OF A CALCIUM-BOUND B-DNA DUPLEX REMARK 900 RELATED ID: 4R4A RELATED DB: PDB REMARK 900 RACEMIC CRYSTAL STRUCTURE OF A COBALT-BOUND B-DNA DUPLEX REMARK 900 RELATED ID: 4R4D RELATED DB: PDB REMARK 900 RACEMIC CRYSTAL STRUCTURE OF A MAGNESIUM-BOUND B-DNA DUPLEX DBREF 4R48 A 1 10 PDB 4R48 4R48 1 10 DBREF 4R48 B 11 20 PDB 4R48 4R48 11 20 SEQRES 1 A 10 DC DC DG DG DT DA DC DC DG DG SEQRES 1 B 10 DC DC DG DG DT DA DC DC DG DG HET NA A 101 1 HET CA B 101 1 HETNAM NA SODIUM ION HETNAM CA CALCIUM ION FORMUL 3 NA NA 1+ FORMUL 4 CA CA 2+ FORMUL 5 HOH *22(H2 O) LINK NA NA A 101 O HOH A 201 1555 1555 2.44 LINK NA NA A 101 O HOH A 204 1555 1555 2.28 LINK NA NA A 101 O HOH A 206 1555 1555 2.53 LINK NA NA A 101 O HOH B 203 1555 1555 2.43 LINK CA CA B 101 O HOH B 201 1555 1555 2.56 LINK CA CA B 101 O HOH B 202 1555 1555 2.61 LINK CA CA B 101 O HOH B 204 1555 1555 2.22 LINK CA CA B 101 O HOH B 205 1555 1555 2.17 LINK CA CA B 101 O HOH B 206 1555 1555 2.53 LINK CA CA B 101 O HOH B 207 1555 1555 2.48 CRYST1 65.950 23.355 72.907 90.00 115.47 90.00 C 1 2/c 1 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 0.015163 0.000000 0.007223 0.00000 SCALE2 0.000000 0.042817 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015193 0.00000