HEADER DNA 28-DEC-10 3Q5C TITLE CRYSTAL STRUCTURE OF FOUR-WAY JUNCTION WITH STICKY END COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*GP*CP*GP*GP*CP*CP*GP*C)-3'); COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS STICKY END, DNA EXPDTA X-RAY DIFFRACTION AUTHOR S.VENKADESH,P.K.MANDAL,N.GAUTHAM REVDAT 2 01-NOV-23 3Q5C 1 REMARK REVDAT 1 18-MAY-11 3Q5C 0 JRNL AUTH S.VENKADESH,P.K.MANDAL,N.GAUTHAM JRNL TITL THE SEQUENCE D(CGGCGGCCGC) SELF-ASSEMBLES INTO A TWO JRNL TITL 2 DIMENSIONAL RHOMBIC DNA LATTICE JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 407 548 2011 JRNL REFN ISSN 0006-291X JRNL PMID 21419105 JRNL DOI 10.1016/J.BBRC.2011.03.056 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6_289) 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.4 REMARK 3 NUMBER OF REFLECTIONS : 3449 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.243 REMARK 3 R VALUE (WORKING SET) : 0.241 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.330 REMARK 3 FREE R VALUE TEST SET COUNT : 145 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE 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 : 0.32 REMARK 3 B_SOL : 35.60 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.000 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 41.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 27.90580 REMARK 3 B22 (A**2) : -27.27910 REMARK 3 B33 (A**2) : -0.62670 REMARK 3 B12 (A**2) : 5.28490 REMARK 3 B13 (A**2) : -8.37940 REMARK 3 B23 (A**2) : 4.19630 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 : 0.016 904 REMARK 3 ANGLE : 2.739 1388 REMARK 3 CHIRALITY : 0.110 156 REMARK 3 PLANARITY : 0.008 40 REMARK 3 DIHEDRAL : 36.143 384 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 3Q5C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1000063213. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-10 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) : 0.9922 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3490 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 36.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : 0.13000 REMARK 200 FOR THE DATA SET : 3.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.2 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.27800 REMARK 200 R SYM FOR SHELL (I) : 0.39300 REMARK 200 FOR SHELL : 1.400 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 1P4Y REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1MM DNA, 50MM CACODYLATE BUFFER, 50MM REMARK 280 CACL2, 1MM SPERMINE, 50% MPD IN RESERVIOR, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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: 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 DC C 1 O3' DC C 1 C3' -0.036 REMARK 500 DC D 1 C5' DC D 1 C4' 0.043 REMARK 500 REMARK 500 REMARK: NULL 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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG A 5 C3' - O3' - P ANGL. DEV. = 13.3 DEGREES REMARK 500 DG A 6 O3' - P - O5' ANGL. DEV. = -12.8 DEGREES REMARK 500 DG A 6 C5' - C4' - O4' ANGL. DEV. = 6.8 DEGREES REMARK 500 DG A 6 C5 - C6 - O6 ANGL. DEV. = -3.9 DEGREES REMARK 500 DC A 7 C5' - C4' - O4' ANGL. DEV. = 7.0 DEGREES REMARK 500 DC A 8 O4' - C1' - N1 ANGL. DEV. = -4.8 DEGREES REMARK 500 DC A 10 O4' - C1' - N1 ANGL. DEV. = -7.7 DEGREES REMARK 500 DC B 1 O4' - C1' - N1 ANGL. DEV. = 10.0 DEGREES REMARK 500 DC B 1 C3' - O3' - P ANGL. DEV. = 14.1 DEGREES REMARK 500 DC B 4 P - O5' - C5' ANGL. DEV. = -9.9 DEGREES REMARK 500 DC B 4 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG B 5 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG B 6 O3' - P - OP1 ANGL. DEV. = 8.2 DEGREES REMARK 500 DG B 6 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC B 7 O4' - C1' - C2' ANGL. DEV. = -6.6 DEGREES REMARK 500 DC B 7 N1 - C1' - C2' ANGL. DEV. = 8.5 DEGREES REMARK 500 DC B 7 O4' - C1' - N1 ANGL. DEV. = -5.6 DEGREES REMARK 500 DC B 8 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 DC B 8 C4' - C3' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 DG B 9 O4' - C4' - C3' ANGL. DEV. = -3.7 DEGREES REMARK 500 DG B 9 C4' - C3' - C2' ANGL. DEV. = -4.3 DEGREES REMARK 500 DG B 9 C3' - C2' - C1' ANGL. DEV. = -7.9 DEGREES REMARK 500 DG B 9 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC B 10 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG C 2 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG C 3 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 DC C 4 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 DG C 5 O4' - C1' - N9 ANGL. DEV. = -4.6 DEGREES REMARK 500 DG C 5 C4 - C5 - N7 ANGL. DEV. = -2.6 DEGREES REMARK 500 DG C 6 O5' - C5' - C4' ANGL. DEV. = -9.7 DEGREES REMARK 500 DG C 6 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DC C 7 O4' - C4' - C3' ANGL. DEV. = -4.0 DEGREES REMARK 500 DC C 7 C3' - C2' - C1' ANGL. DEV. = -6.3 DEGREES REMARK 500 DC C 7 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 DC C 7 C3' - O3' - P ANGL. DEV. = 10.6 DEGREES REMARK 500 DG C 9 O5' - C5' - C4' ANGL. DEV. = -8.3 DEGREES REMARK 500 DG C 9 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 DC D 1 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 DC D 1 C3' - C2' - C1' ANGL. DEV. = -10.6 DEGREES REMARK 500 DC D 1 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 DC D 1 C3' - O3' - P ANGL. DEV. = 11.5 DEGREES REMARK 500 DG D 2 O3' - P - OP2 ANGL. DEV. = 7.1 DEGREES REMARK 500 DG D 2 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 DG D 2 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 DG D 3 O4' - C4' - C3' ANGL. DEV. = -4.3 DEGREES REMARK 500 DG D 3 C4' - C3' - C2' ANGL. DEV. = -5.8 DEGREES REMARK 500 DC D 7 C4' - C3' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 DG D 9 O4' - C4' - C3' ANGL. DEV. = -2.9 DEGREES REMARK 500 DC D 10 O4' - C1' - N1 ANGL. DEV. = 8.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 3Q5C A 1 10 PDB 3Q5C 3Q5C 1 10 DBREF 3Q5C B 1 10 PDB 3Q5C 3Q5C 1 10 DBREF 3Q5C C 1 10 PDB 3Q5C 3Q5C 1 10 DBREF 3Q5C D 1 10 PDB 3Q5C 3Q5C 1 10 SEQRES 1 A 10 DC DG DG DC DG DG DC DC DG DC SEQRES 1 B 10 DC DG DG DC DG DG DC DC DG DC SEQRES 1 C 10 DC DG DG DC DG DG DC DC DG DC SEQRES 1 D 10 DC DG DG DC DG DG DC DC DG DC FORMUL 5 HOH *9(H2 O) CRYST1 23.640 33.841 40.400 112.77 90.00 110.44 P 1 4 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 0.042301 0.015768 0.007152 0.00000 SCALE2 0.000000 0.031536 0.014305 0.00000 SCALE3 0.000000 0.000000 0.027180 0.00000