HEADER DNA 29-MAY-18 6GN3 TITLE RACEMIC CRYSTAL STRUCTURE OF A-DNA DUPLEX FORMED FROM D(CCCGGG) IN TITLE 2 SPACE GROUP P21/N COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*CP*CP*GP*GP*G)-3'); COMPND 3 CHAIN: A, B, C, D, E, F; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: RACEMIC DNA SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS RACEMATE, DNA EXPDTA X-RAY DIFFRACTION AUTHOR P.K.MANDAL,G.W.COLLIE,B.KAUFFMANN,I.HUC REVDAT 3 17-JAN-24 6GN3 1 REMARK REVDAT 2 25-SEP-19 6GN3 1 REMARK REVDAT 1 11-SEP-19 6GN3 0 JRNL AUTH P.K.MANDAL,G.W.COLLIE,B.KAUFFMANN,I.HUC JRNL TITL RACEMIC CRYSTAL STRUCTURES OF A-DNA DUPLEXES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.K.MANDAL,G.W.COLLIE,B.KAUFFMANN,I.HUC REMARK 1 TITL RACEMIC DNA CRYSTALLOGRAPHY REMARK 1 REF ANGEW. CHEM. INT. ED. V. 53 14424 2014 REMARK 1 REFN ISSN 1433-7851 REMARK 1 PMID 25358289 REMARK 1 DOI 10.1002/ANIE.201409014 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 6804 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.284 REMARK 3 R VALUE (WORKING SET) : 0.280 REMARK 3 FREE R VALUE : 0.318 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.040 REMARK 3 FREE R VALUE TEST SET COUNT : 683 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 31.4947 - 4.7836 0.99 1229 137 0.2276 0.2349 REMARK 3 2 4.7836 - 3.7990 0.97 1197 134 0.2608 0.2794 REMARK 3 3 3.7990 - 3.3194 1.00 1242 138 0.2868 0.3709 REMARK 3 4 3.3194 - 3.0161 0.99 1238 138 0.3168 0.3516 REMARK 3 5 3.0161 - 2.8001 0.99 1215 136 0.4187 0.5296 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.460 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.82 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.17 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 : 0.007 820 REMARK 3 ANGLE : 0.561 1254 REMARK 3 CHIRALITY : 0.030 138 REMARK 3 PLANARITY : 0.003 36 REMARK 3 DIHEDRAL : 14.448 336 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): -75.7742 -42.6979 10.9239 REMARK 3 T TENSOR REMARK 3 T11: 0.3531 T22: 0.5920 REMARK 3 T33: 0.2583 T12: 0.0018 REMARK 3 T13: -0.0067 T23: -0.0264 REMARK 3 L TENSOR REMARK 3 L11: 1.7038 L22: 1.3106 REMARK 3 L33: 2.7820 L12: 0.4675 REMARK 3 L13: -2.1435 L23: -0.8939 REMARK 3 S TENSOR REMARK 3 S11: -0.3152 S12: -1.0104 S13: -0.3627 REMARK 3 S21: 0.0125 S22: 0.0792 S23: 0.0687 REMARK 3 S31: 0.1856 S32: -0.8499 S33: 0.2261 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 7 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): -76.2885 -35.8928 7.6057 REMARK 3 T TENSOR REMARK 3 T11: 0.2665 T22: 0.4473 REMARK 3 T33: 0.1929 T12: -0.0488 REMARK 3 T13: 0.0419 T23: -0.0661 REMARK 3 L TENSOR REMARK 3 L11: 2.4552 L22: 2.4201 REMARK 3 L33: 2.4010 L12: -1.9581 REMARK 3 L13: -0.8885 L23: -0.4693 REMARK 3 S TENSOR REMARK 3 S11: 0.4423 S12: -0.2995 S13: 0.0514 REMARK 3 S21: -0.3224 S22: 0.1620 S23: -0.2190 REMARK 3 S31: -0.4071 S32: -0.2319 S33: -0.4964 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): -83.5464 -26.5776 21.4134 REMARK 3 T TENSOR REMARK 3 T11: 0.4386 T22: 0.5856 REMARK 3 T33: 0.3540 T12: 0.0427 REMARK 3 T13: 0.0591 T23: -0.1190 REMARK 3 L TENSOR REMARK 3 L11: 0.4547 L22: 7.5210 REMARK 3 L33: 1.4992 L12: 0.2011 REMARK 3 L13: 0.1160 L23: 3.3577 REMARK 3 S TENSOR REMARK 3 S11: -0.0306 S12: -0.4879 S13: 0.3925 REMARK 3 S21: 1.1916 S22: 0.1762 S23: 0.3002 REMARK 3 S31: 0.6101 S32: -0.0360 S33: -0.1997 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 7 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): -81.1072 -22.8864 15.4779 REMARK 3 T TENSOR REMARK 3 T11: 0.4528 T22: 0.6519 REMARK 3 T33: 0.3052 T12: -0.0668 REMARK 3 T13: 0.1193 T23: -0.1399 REMARK 3 L TENSOR REMARK 3 L11: 4.3861 L22: 6.2204 REMARK 3 L33: 0.8360 L12: -2.4889 REMARK 3 L13: -1.9136 L23: 0.9869 REMARK 3 S TENSOR REMARK 3 S11: 0.7586 S12: -0.2535 S13: 0.6116 REMARK 3 S21: -0.6477 S22: -0.3827 S23: -0.6136 REMARK 3 S31: -0.1652 S32: -0.8474 S33: -0.4017 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'E' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): -68.9895 -23.0976 27.8493 REMARK 3 T TENSOR REMARK 3 T11: 0.5500 T22: 0.5569 REMARK 3 T33: 0.4770 T12: -0.0100 REMARK 3 T13: -0.1159 T23: -0.1331 REMARK 3 L TENSOR REMARK 3 L11: 7.0431 L22: 2.6586 REMARK 3 L33: 4.0655 L12: -0.3713 REMARK 3 L13: 1.2221 L23: -0.8923 REMARK 3 S TENSOR REMARK 3 S11: -0.0835 S12: 0.2260 S13: 0.3844 REMARK 3 S21: -0.2176 S22: -0.4143 S23: 0.8003 REMARK 3 S31: -0.2828 S32: -0.6543 S33: 0.4192 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'F' AND (RESID 7 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): -65.6542 -25.1171 21.7371 REMARK 3 T TENSOR REMARK 3 T11: 0.3322 T22: 1.2569 REMARK 3 T33: 0.4812 T12: -0.0389 REMARK 3 T13: -0.1025 T23: -0.0209 REMARK 3 L TENSOR REMARK 3 L11: 2.5062 L22: 3.5407 REMARK 3 L33: 1.3635 L12: 2.8428 REMARK 3 L13: 0.9499 L23: 1.1773 REMARK 3 S TENSOR REMARK 3 S11: -0.1893 S12: 1.7779 S13: 0.0866 REMARK 3 S21: -0.3538 S22: 0.1837 S23: -0.0983 REMARK 3 S31: -0.1072 S32: 1.0060 S33: 0.4105 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6GN3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1200010270. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-AUG-15 REMARK 200 TEMPERATURE (KELVIN) : 150 REMARK 200 PH : 6.5 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 FR-X REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5417 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6839 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 31.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.07290 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.33930 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.470 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: 1VT5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, MES BUFFER, COBALT REMARK 280 CHLORIDE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21/n 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 3555 -X,-Y,-Z REMARK 290 4555 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 19.76398 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 20.71500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 35.67365 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 19.76398 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.71500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.67365 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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 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 B 11 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6GN2 RELATED DB: PDB REMARK 900 RACEMIC STRUCTURE IN THE SPACE GROUP R-3 DBREF 6GN3 A 1 6 PDB 6GN3 6GN3 1 6 DBREF 6GN3 B 7 12 PDB 6GN3 6GN3 7 12 DBREF 6GN3 C 1 6 PDB 6GN3 6GN3 1 6 DBREF 6GN3 D 7 12 PDB 6GN3 6GN3 7 12 DBREF 6GN3 E 1 6 PDB 6GN3 6GN3 1 6 DBREF 6GN3 F 7 12 PDB 6GN3 6GN3 7 12 SEQRES 1 A 6 DC DC DC DG DG DG SEQRES 1 B 6 DC DC DC DG DG DG SEQRES 1 C 6 DC DC DC DG DG DG SEQRES 1 D 6 DC DC DC DG DG DG SEQRES 1 E 6 DC DC DC DG DG DG SEQRES 1 F 6 DC DC DC DG DG DG HET TMO A 101 5 HET TMO A 102 5 HET CO B 101 1 HET TMO B 102 5 HET CL C 101 1 HET CO D 101 1 HET TMO F 101 5 HETNAM TMO TRIMETHYLAMINE OXIDE HETNAM CO COBALT (II) ION HETNAM CL CHLORIDE ION FORMUL 7 TMO 4(C3 H9 N O) FORMUL 9 CO 2(CO 2+) FORMUL 11 CL CL 1- FORMUL 14 HOH *8(H2 O) LINK N7 DG B 11 CO CO B 101 1555 1555 2.37 LINK N7 DG D 11 CO CO D 101 1555 1555 2.34 CRYST1 48.883 41.430 71.958 90.00 97.47 90.00 P 1 21/n 1 24 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 0.020457 0.000000 0.002681 0.00000 SCALE2 0.000000 0.024137 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014016 0.00000