10 20 30 40 50 60 70 80 4OKL - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 22-JAN-14 4OKL
TITLE CRYSTAL STRUCTURE OF D(CCCCGGTACCGGGG)2 AT 1.65 ANGSTROM
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 14 MER A-DNA; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED OLIGO NUCLEOTIDE FRAGMENT.
KEYWDS A-DNA, TETRA-DECANUCLEOTIDE, CRYSTAL PACKING, RIGHT HANDED, DOUBLE KEYWDS 2 HELIX, DNA
EXPDTA X-RAY DIFFRACTION
AUTHOR V.ANNA,P.MONICA,P.K.MANDAL,N.GAUTHAM
REVDAT 2 10-DEC-14 4OKL 1 JRNL REVDAT 1 19-FEB-14 4OKL 0
JRNL AUTH M.PURUSHOTHAMAN,A.VARGHESE,P.K.MANDAL,N.GAUTHAM JRNL TITL STRUCTURE OF D(CCCCGGTACCGGGG)2 AT 1.65 ANGSTROM RESOLUTION. JRNL REF ACTA CRYSTALLOGR F STRUCT V. 70 860 2014 JRNL REF 2 BIOL COMMUN JRNL REFN ISSN 1744-3091 JRNL PMID 25005078 JRNL DOI 10.1107/S2053230X1401084X
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.VENKADESH,P.K.MANDAL,N.GAUTHAM REMARK 1 TITL THE STRUCTURE OF A FULL TURN OF AN A-DNA DUPLEX REMARK 1 TITL 2 D(CGCGGGTACCCGCG)2. REMARK 1 REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 407 307 2011 REMARK 1 REFN ISSN 0006-291X REMARK 1 PMID 21397589 REMARK 1 DOI 10.1016/J.BBRC.2011.03.007 REMARK 1 REFERENCE 2 REMARK 1 AUTH P.K.MANDAL,S.VENKADESH,N.GAUTHAM REMARK 1 TITL STRUCTURE OF THE TETRADECANUCLEOTIDE D(CCCCGGTACCGGGG)2 AS REMARK 1 TITL 2 AN A-DNA DUPLEX. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 68 393 2012 REMARK 1 REFN ISSN 1744-3091 REMARK 1 PMID 22505405 REMARK 1 DOI 10.1107/S174430911200869X
REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 9654 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 964 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 30.0531 - 3.1554 0.99 1348 150 0.1831 0.1759 REMARK 3 2 3.1554 - 2.5050 1.00 1256 138 0.2539 0.2839 REMARK 3 3 2.5050 - 2.1884 1.00 1237 137 0.2644 0.2707 REMARK 3 4 2.1884 - 1.9884 1.00 1227 136 0.2753 0.2940 REMARK 3 5 1.9884 - 1.8459 1.00 1223 137 0.2658 0.3323 REMARK 3 6 1.8459 - 1.7371 1.00 1211 135 0.2587 0.3033 REMARK 3 7 1.7371 - 1.6501 1.00 1188 131 0.2228 0.2647 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.570 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.003 636 REMARK 3 ANGLE : 0.846 978 REMARK 3 CHIRALITY : 0.033 110 REMARK 3 PLANARITY : 0.002 28 REMARK 3 DIHEDRAL : 16.582 272 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: chain 'A' and (resid 1 through 14 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.5823 12.0202 23.3993 REMARK 3 T TENSOR REMARK 3 T11: 0.1935 T22: 0.3024 REMARK 3 T33: 0.2661 T12: 0.0370 REMARK 3 T13: 0.0098 T23: -0.0221 REMARK 3 L TENSOR REMARK 3 L11: 1.2664 L22: 2.3356 REMARK 3 L33: 5.9608 L12: 0.9078 REMARK 3 L13: -0.2788 L23: -3.4059 REMARK 3 S TENSOR REMARK 3 S11: 0.0234 S12: 0.2323 S13: 0.0572 REMARK 3 S21: 0.0196 S22: 0.1263 S23: 0.1409 REMARK 3 S31: -0.0380 S32: -0.2980 S33: -0.1513 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: chain 'B' and (resid 1 through 14 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.2229 11.7887 20.5773 REMARK 3 T TENSOR REMARK 3 T11: 0.2590 T22: 0.3357 REMARK 3 T33: 0.2803 T12: 0.0276 REMARK 3 T13: -0.0091 T23: 0.0449 REMARK 3 L TENSOR REMARK 3 L11: 5.2683 L22: 1.8366 REMARK 3 L33: 2.4457 L12: 1.4676 REMARK 3 L13: -1.2619 L23: 0.4985 REMARK 3 S TENSOR REMARK 3 S11: 0.0298 S12: 0.8860 S13: 0.2783 REMARK 3 S21: -0.1578 S22: 0.1950 S23: 0.0600 REMARK 3 S31: -0.0663 S32: -0.1599 S33: -0.2360 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 4OKL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JAN-14. REMARK 100 THE RCSB ID CODE IS RCSB084610.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUL-12 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 : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95372 REMARK 200 MONOCHROMATOR : SI (111) MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9714 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 30.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.650 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.800 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1357.00 REMARK 200 R MERGE FOR SHELL (I) : 40.90000 REMARK 200 R SYM FOR SHELL (I) : 14.10000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.700 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: PDB ENTRY 3V9D REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1MM DNA, 50MM SODIUM CACODYLATE REMARK 280 BUFFER, 10MM ZNCL2, 10MM SPERMINE, 33% MPD (V/V), PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.83500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 20.63500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 20.63500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.91750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 20.63500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 20.63500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 65.75250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 20.63500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 20.63500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 21.91750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 20.63500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 20.63500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 65.75250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 43.83500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL 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 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG B 6 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DC B 9 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG B 13 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3V9D RELATED DB: PDB REMARK 900 RELATED ID: 3QK4 RELATED DB: PDB
DBREF 4OKL A 1 14 PDB 4OKL 4OKL 1 14 DBREF 4OKL B 1 14 PDB 4OKL 4OKL 1 14
SEQRES 1 A 14 DC DC DC DC DG DG DT DA DC DC DG DG DG SEQRES 2 A 14 DG SEQRES 1 B 14 DC DC DC DC DG DG DT DA DC DC DG DG DG SEQRES 2 B 14 DG
FORMUL 3 HOH *44(H2 O)
CRYST1 41.270 41.270 87.670 90.00 90.00 90.00 P 41 21 2 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 0.024231 0.000000 0.000000 0.00000
SCALE2 0.000000 0.024231 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011406 0.00000