HEADER DNA 06-JUN-14 4QKK TITLE CRYSTAL STRUCTURE OF AN OLIGONUCLEOTIDE CONTAINING 5-FORMYLCYTOSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*TP*AP*(5FC)P*GP*(5FC)P*GP*(5FC)P*GP*TP*AP*G)- COMPND 3 3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS OLIGONUCLEOTIDE, EPIGENETIC TEN-ELEVEN, TRANSLOCATION PROTEINS, KEYWDS 2 THYMINE DNA GLYCOSYLASE, FORMYLCYTOSINE, DNA EXPDTA X-RAY DIFFRACTION AUTHOR E.-A.RAIBER,P.MURAT,D.Y.CHIRGADZE,B.F.LUISI,S.BALASUBRAMANIAN REVDAT 3 20-MAR-24 4QKK 1 REMARK REVDAT 2 25-DEC-19 4QKK 1 SOURCE JRNL LINK REVDAT 1 10-DEC-14 4QKK 0 JRNL AUTH E.A.RAIBER,P.MURAT,D.Y.CHIRGADZE,D.BERALDI,B.F.LUISI, JRNL AUTH 2 S.BALASUBRAMANIAN JRNL TITL 5-FORMYLCYTOSINE ALTERS THE STRUCTURE OF THE DNA DOUBLE JRNL TITL 2 HELIX. JRNL REF NAT.STRUCT.MOL.BIOL. V. 22 44 2015 JRNL REFN ESSN 1545-9985 JRNL PMID 25504322 JRNL DOI 10.1038/NSMB.2936 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 9567 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.141 REMARK 3 R VALUE (WORKING SET) : 0.140 REMARK 3 FREE R VALUE : 0.159 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 479 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 25.9784 - 2.0190 1.00 3148 165 0.1288 0.1465 REMARK 3 2 2.0190 - 1.6026 1.00 2986 162 0.1631 0.1650 REMARK 3 3 1.6026 - 1.4000 1.00 2954 152 0.2104 0.2960 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.420 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.90 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 : 0.014 278 REMARK 3 ANGLE : 1.377 427 REMARK 3 CHIRALITY : 0.080 44 REMARK 3 PLANARITY : 0.011 12 REMARK 3 DIHEDRAL : 23.801 101 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 4QKK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1000086171. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-APR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9686 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9608 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 46.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.10 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : 0.06000 REMARK 200 FOR THE DATA SET : 19.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.20 REMARK 200 R MERGE FOR SHELL (I) : 0.17150 REMARK 200 R SYM FOR SHELL (I) : 0.17150 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: P-SAD REMARK 200 SOFTWARE USED: PHENIX 1.9_1692 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.01M MAGNESIUM SULPHATE, 0.05M SODIUM REMARK 280 CACODYLATE, 1.8M LITHIUM SULPHATE, PH 6.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 23.12700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 22.19650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 22.19650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 34.69050 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 22.19650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 22.19650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 11.56350 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 22.19650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 22.19650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 34.69050 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 22.19650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 22.19650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 11.56350 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 23.12700 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 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 BIOMT1 2 0.000000 -1.000000 0.000000 44.39300 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 44.39300 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 23.12700 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 DG A 9 O3' DG A 9 C3' -0.044 REMARK 500 DT A 10 O3' DT A 10 C3' -0.042 REMARK 500 REMARK 500 REMARK: NULL DBREF 4QKK A 1 12 PDB 4QKK 4QKK 1 12 SEQRES 1 A 12 DC DT DA 5FC DG 5FC DG 5FC DG DT DA DG MODRES 4QKK 5FC A 4 DC MODRES 4QKK 5FC A 6 DC MODRES 4QKK 5FC A 8 DC HET 5FC A 4 32 HET 5FC A 6 32 HET 5FC A 8 32 HETNAM 5FC 5-FORMYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETSYN 5FC 2'-DEOXY-5-FORMYLCYTIDINE-5'-MONOPHOSPHATE FORMUL 1 5FC 3(C10 H14 N3 O8 P) FORMUL 2 HOH *54(H2 O) LINK O3' DA A 3 P 5FC A 4 1555 1555 1.61 LINK O3' 5FC A 4 P DG A 5 1555 1555 1.62 LINK O3' DG A 5 P 5FC A 6 1555 1555 1.59 LINK O3' 5FC A 6 P DG A 7 1555 1555 1.62 LINK O3' DG A 7 P 5FC A 8 1555 1555 1.61 LINK O3' 5FC A 8 P DG A 9 1555 1555 1.61 CRYST1 44.393 44.393 46.254 90.00 90.00 90.00 P 43 21 2 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 0.022526 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022526 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021620 0.00000