HEADER DNA 10-SEP-10 3OT0 TITLE CRYSTAL STRUCTURE OF A DNA CONTAINING THE RIGID NITROXIDE SPIN-LABELED TITLE 2 NUCLEOTIDE C-SPIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIN-LABELED DNA; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICAL SYNTHESIS KEYWDS NITROXIDE, SPIN-LABEL, EPR SPECTROSCOPY, FLUORESCENCE SPECTROSCOPY, KEYWDS 2 MODIFIED NUCLEIC ACID, C-SPIN, DEOXYCYTOSINE ANALOG, PHENOXAZINE, KEYWDS 3 SPECTROSCOPIC PROBE, PELDOR, 2'-O-METHYL U, DNA EXPDTA X-RAY DIFFRACTION AUTHOR T.E.EDWARDS REVDAT 4 06-SEP-23 3OT0 1 REMARK REVDAT 3 22-JUL-20 3OT0 1 REMARK HETNAM LINK REVDAT 2 08-JUN-11 3OT0 1 JRNL REVDAT 1 19-JAN-11 3OT0 0 JRNL AUTH T.E.EDWARDS,P.CEKAN,G.W.REGINSSON,S.A.SHELKE, JRNL AUTH 2 A.R.FERRE-D'AMARE,O.SCHIEMANN,S.T.SIGURDSSON JRNL TITL CRYSTAL STRUCTURE OF A DNA CONTAINING THE PLANAR, JRNL TITL 2 PHENOXAZINE-DERIVED BI-FUNCTIONAL SPECTROSCOPIC PROBE C. JRNL REF NUCLEIC ACIDS RES. V. 10 4419 2011 JRNL REFN ISSN 0305-1048 JRNL PMID 21252294 JRNL DOI 10.1093/NAR/GKR015 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.1_357) 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 3 NUMBER OF REFLECTIONS : 5586 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.540 REMARK 3 FREE R VALUE TEST SET COUNT : 533 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 16.8246 - 2.6964 0.99 1405 148 0.1557 0.1728 REMARK 3 2 2.6964 - 2.1416 0.98 1290 152 0.1770 0.2186 REMARK 3 3 2.1416 - 1.8713 0.94 1253 117 0.1584 0.2342 REMARK 3 4 1.8713 - 1.7004 0.85 1105 116 0.1380 0.2182 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 : 0.41 REMARK 3 B_SOL : 45.02 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.500 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) : -0.04390 REMARK 3 B22 (A**2) : -0.38630 REMARK 3 B33 (A**2) : 0.43020 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 : 0.007 490 REMARK 3 ANGLE : 1.738 762 REMARK 3 CHIRALITY : 0.067 80 REMARK 3 PLANARITY : 0.007 22 REMARK 3 DIHEDRAL : 25.722 208 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 3OT0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-OCT-10. REMARK 100 THE DEPOSITION ID IS D_1000061535. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-APR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 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-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : VARIMAX REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5613 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 200 DATA REDUNDANCY : 8.400 REMARK 200 R MERGE (I) : 0.02200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 53.9500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.07000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 20.03 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 1KGK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2 MM DNA IN 10% 2-METHANE-2,4 REMARK 280 -PENTANEDIOL (MPD), 40 MM SODIUM CACODYLATE PH 6.0, 12 MM REMARK 280 SPERMINE-HCL, 80 MM NACL, 12 MM KCL, 12 MM MGCL2 AGAINST A REMARK 280 RESERVIORE OF 35% MPD, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 12.35500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.97000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.27500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.97000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.35500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.27500 REMARK 290 SMTRY3 4 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: 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 DG A 9 C3' - C2' - C1' ANGL. DEV. = -5.1 DEGREES REMARK 500 DG B 3 O4' - C4' - C3' ANGL. DEV. = -3.2 DEGREES REMARK 500 DC B 8 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DPL RELATED DB: PDB REMARK 900 SAME SEQUENCE CONTAINING A C AT POSITION 2 AND A 2'-O-METHOXYMETHYL REMARK 900 T AT POSITION 6 REMARK 900 RELATED ID: 1KGK RELATED DB: PDB REMARK 900 SAME SEQUENCE CONTAINING A PHENOXAZINE-DERIVED G-CLAMP MODIFIED C REMARK 900 AT POSITION 2 AND A 2'-O-METHOXYMETHYL T AT POSITION 6 DBREF 3OT0 A 1 10 PDB 3OT0 3OT0 1 10 DBREF 3OT0 B 1 10 PDB 3OT0 3OT0 1 10 SEQRES 1 A 10 DG EXC DG DT DA OMU DA DC DG DC SEQRES 1 B 10 DG EXC DG DT DA OMU DA DC DG DC MODRES 3OT0 EXC A 2 DC MODRES 3OT0 OMU A 6 U O2'-METHYLURIDINE 5'-MONOPHOSPHATE MODRES 3OT0 EXC B 2 DC MODRES 3OT0 OMU B 6 U O2'-METHYLURIDINE 5'-MONOPHOSPHATE HET EXC A 2 34 HET OMU A 6 21 HET EXC B 2 34 HET OMU B 6 21 HETNAM EXC 3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO- HETNAM 2 EXC PENTOFURANOSYL)-8-HYDROXY-7,7,9,9-TETRAMETHYL-7,8,9, HETNAM 3 EXC 11-TETRAHYDROPYRIMIDO[4',5' :5,6][1,4]OXAZINO[2,3- HETNAM 4 EXC F]ISOINDOL-2(3H)-ONE RADICAL HETNAM OMU O2'-METHYLURIDINE 5'-MONOPHOSPHATE HETSYN EXC NITROXIDE SPIN-LABELED NUCLEOTIDE C-SPIN FORMUL 1 EXC 2(C21 H26 N4 O9 P) FORMUL 1 OMU 2(C10 H15 N2 O9 P) FORMUL 3 HOH *83(H2 O) LINK O3' DG A 1 P EXC A 2 1555 1555 1.61 LINK O3' DA A 5 P OMU A 6 1555 1555 1.60 LINK O3' OMU A 6 P DA A 7 1555 1555 1.60 LINK O3' DG B 1 P EXC B 2 1555 1555 1.60 LINK O3' DA B 5 P OMU B 6 1555 1555 1.60 LINK O3' OMU B 6 P DA B 7 1555 1555 1.61 CRYST1 24.710 44.550 45.940 90.00 90.00 90.00 P 21 21 21 8 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 0.040469 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022447 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021768 0.00000