HEADER DNA 15-JAN-15 4XNO TITLE CRYSTAL STRUCTURE OF 5'-CTTATPPPZZZATAAG COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*TP*(BRU)P*AP*TP*(1WA)P*(1WA)P*(1WA)P*(1W5) COMPND 3 P*(1W5)P*(1W5)P*AP*TP*AP*AP*G)-3'); COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS A-FORM DNA, NON-NATURAL NUCLEOBASE PAIR, SYNTHETIC BIOLOGY, DNA EXPDTA X-RAY DIFFRACTION AUTHOR M.M.GEORGIADIS,I.SINGH REVDAT 6 28-FEB-24 4XNO 1 REMARK REVDAT 5 25-DEC-19 4XNO 1 REMARK REVDAT 4 20-SEP-17 4XNO 1 REMARK REVDAT 3 11-JAN-17 4XNO 1 JRNL REVDAT 2 18-MAY-16 4XNO 1 HETNAM REVDAT 1 27-MAY-15 4XNO 0 JRNL AUTH M.M.GEORGIADIS,I.SINGH,W.F.KELLETT,S.HOSHIKA,S.A.BENNER, JRNL AUTH 2 N.G.RICHARDS JRNL TITL STRUCTURAL BASIS FOR A SIX NUCLEOTIDE GENETIC ALPHABET. JRNL REF J. AM. CHEM. SOC. V. 137 6947 2015 JRNL REFN ESSN 1520-5126 JRNL PMID 25961938 JRNL DOI 10.1021/JACS.5B03482 REMARK 2 REMARK 2 RESOLUTION. 1.99 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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.23 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 10129 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.750 REMARK 3 FREE R VALUE TEST SET COUNT : 481 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 35.2323 - 2.8623 0.99 3490 151 0.1859 0.1922 REMARK 3 2 2.8623 - 2.2720 1.00 3275 188 0.2424 0.2958 REMARK 3 3 2.2720 - 1.9848 0.88 2883 142 0.2646 0.2974 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 : 0.42 REMARK 3 B_SOL : 49.68 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.570 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.05 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.44720 REMARK 3 B22 (A**2) : -2.44720 REMARK 3 B33 (A**2) : 4.65770 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 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 : 0.003 746 REMARK 3 ANGLE : 0.829 1078 REMARK 3 CHIRALITY : 0.035 70 REMARK 3 PLANARITY : 0.025 46 REMARK 3 DIHEDRAL : 16.672 426 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 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4XNO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000205918. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUL-14 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91963 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10571 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.76800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD 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 (%): 64.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 93.64800 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 46.82400 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 46.82400 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 93.64800 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 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 BRU A 3 O3' - P - O5' ANGL. DEV. = -13.3 DEGREES REMARK 500 DT A 5 C3' - O3' - P ANGL. DEV. = -11.3 DEGREES REMARK 500 1WA A 6 O3' - P - OP2 ANGL. DEV. = 11.6 DEGREES REMARK 500 1WA A 7 O3' - P - OP2 ANGL. DEV. = 8.4 DEGREES REMARK 500 1W5 A 10 O3' - P - OP1 ANGL. DEV. = -15.0 DEGREES REMARK 500 1W5 A 11 O3' - P - OP1 ANGL. DEV. = -17.2 DEGREES REMARK 500 1W5 A 11 C3' - O3' - P ANGL. DEV. = -15.8 DEGREES REMARK 500 DA A 12 O3' - P - O5' ANGL. DEV. = 15.1 DEGREES REMARK 500 DA A 12 O3' - P - OP2 ANGL. DEV. = 14.9 DEGREES REMARK 500 DA A 12 O3' - P - OP1 ANGL. DEV. = -35.5 DEGREES REMARK 500 BRU B 3 C3' - O3' - P ANGL. DEV. = -15.9 DEGREES REMARK 500 1WA B 7 O3' - P - OP2 ANGL. DEV. = 9.8 DEGREES REMARK 500 1W5 B 9 O3' - P - OP1 ANGL. DEV. = -13.8 DEGREES REMARK 500 1W5 B 10 O3' - P - OP1 ANGL. DEV. = -15.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4XO0 RELATED DB: PDB REMARK 900 RELATED ID: 4XPC RELATED DB: PDB REMARK 900 RELATED ID: 4XPE RELATED DB: PDB DBREF 4XNO A 1 16 PDB 4XNO 4XNO 1 16 DBREF 4XNO B 1 16 PDB 4XNO 4XNO 1 16 SEQRES 1 A 16 DC DT BRU DA DT 1WA 1WA 1WA 1W5 1W5 1W5 DA DT SEQRES 2 A 16 DA DA DG SEQRES 1 B 16 DC DT BRU DA DT 1WA 1WA 1WA 1W5 1W5 1W5 DA DT SEQRES 2 B 16 DA DA DG HET BRU A 3 20 HET 1WA A 6 22 HET 1WA A 7 22 HET 1WA A 8 22 HET 1W5 A 9 22 HET 1W5 A 10 22 HET 1W5 A 11 22 HET BRU B 3 20 HET 1WA B 6 22 HET 1WA B 7 22 HET 1WA B 8 22 HET 1W5 B 9 22 HET 1W5 B 10 22 HET 1W5 B 11 22 HETNAM BRU 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE HETNAM 1WA 2-AMINO-8-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO- HETNAM 2 1WA PENTOFURANOSYL)-4-HYDROXY-1H-IMIDAZO[1,2-A][1,3, HETNAM 3 1WA 5]TRIAZINE-5,8-DIIUM HETNAM 1W5 (1R)-1-(6-AMINO-2-HYDROXY-5-NITROPYRIDIN-3-YL)-1,4- HETNAM 2 1W5 ANHYDRO-2-DEOXY-5-O-PHOSPHONO-D-ERYTHRO-PENTITOL FORMUL 1 BRU 2(C9 H12 BR N2 O8 P) FORMUL 1 1WA 6(C10 H16 N5 O7 P 2+) FORMUL 1 1W5 6(C10 H14 N3 O9 P) FORMUL 3 HOH *73(H2 O) LINK O3' DT A 2 P BRU A 3 1555 1555 1.59 LINK O3' BRU A 3 P DA A 4 1555 1555 1.59 LINK O3' DT A 5 P 1WA A 6 1555 1555 1.59 LINK O3' 1WA A 6 P 1WA A 7 1555 1555 1.59 LINK O3' 1WA A 7 P 1WA A 8 1555 1555 1.59 LINK O3' 1WA A 8 P 1W5 A 9 1555 1555 1.59 LINK O3' 1W5 A 9 P 1W5 A 10 1555 1555 1.59 LINK O3' 1W5 A 10 P 1W5 A 11 1555 1555 1.59 LINK O3' 1W5 A 11 P DA A 12 1555 1555 1.59 LINK O3' DT B 2 P BRU B 3 1555 1555 1.59 LINK O3' BRU B 3 P DA B 4 1555 1555 1.59 LINK O3' DT B 5 P 1WA B 6 1555 1555 1.59 LINK O3' 1WA B 6 P 1WA B 7 1555 1555 1.59 LINK O3' 1WA B 7 P 1WA B 8 1555 1555 1.59 LINK O3' 1WA B 8 P 1W5 B 9 1555 1555 1.59 LINK O3' 1W5 B 9 P 1W5 B 10 1555 1555 1.59 LINK O3' 1W5 B 10 P 1W5 B 11 1555 1555 1.59 LINK O3' 1W5 B 11 P DA B 12 1555 1555 1.59 CRYST1 42.019 42.019 140.472 90.00 90.00 120.00 P 32 2 1 12 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 0.023799 0.013740 0.000000 0.00000 SCALE2 0.000000 0.027480 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007119 0.00000