HEADER DNA 14-AUG-12 4GLC TITLE DNA DODECAMER CONTAINING 5-HYDROXYMETHYL-CYTOSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*(5HC)P*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS B-DNA DODECAMER, EPIGENETICS, 5-HYDROXYMETHYL CYTOSINE, DNA EXPDTA X-RAY DIFFRACTION AUTHOR B.SPINGLER,D.RENCIUK,M.VORLICKOVA REVDAT 4 13-SEP-23 4GLC 1 LINK REVDAT 3 04-DEC-13 4GLC 1 JRNL REVDAT 2 04-SEP-13 4GLC 1 JRNL REVDAT 1 28-AUG-13 4GLC 0 JRNL AUTH D.RENCIUK,O.BLACQUE,M.VORLICKOVA,B.SPINGLER JRNL TITL CRYSTAL STRUCTURES OF B-DNA DODECAMER CONTAINING THE JRNL TITL 2 EPIGENETIC MODIFICATIONS 5-HYDROXYMETHYLCYTOSINE OR JRNL TITL 3 5-METHYLCYTOSINE. JRNL REF NUCLEIC ACIDS RES. V. 41 9891 2013 JRNL REFN ISSN 0305-1048 JRNL PMID 23963698 JRNL DOI 10.1093/NAR/GKT738 REMARK 2 REMARK 2 RESOLUTION. 1.83 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.251 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.233 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.306 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 7.015 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 435 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 6201 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.244 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.225 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 7.052 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 400 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 5672 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 490 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 40 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 528.60 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 2123 REMARK 3 NUMBER OF RESTRAINTS : 2406 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 ANGLE DISTANCES (A) : 0.028 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.012 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.006 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.008 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.070 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4GLC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000074327. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUN-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 : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00067 REMARK 200 MONOCHROMATOR : BARTELS MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6201 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.831 REMARK 200 RESOLUTION RANGE LOW (A) : 41.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 3.680 REMARK 200 R MERGE (I) : 0.03400 REMARK 200 R SYM (I) : 0.02100 REMARK 200 FOR THE DATA SET : 24.0600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.62 REMARK 200 R MERGE FOR SHELL (I) : 0.21600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.650 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 1DPN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.04M SODIUM CACODYLATE BUFFER, 0.08M REMARK 280 SODIUM CHLORIDE, 0.012M SPERMINE TETRA HYDROCHLORIDE, 30% MPD, REMARK 280 PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 12.25650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.02200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.80100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.02200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.25650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.80100 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4550 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 2 O4' - C1' - N9 ANGL. DEV. = -5.2 DEGREES REMARK 500 DA A 6 O4' - C1' - N9 ANGL. DEV. = -5.1 DEGREES REMARK 500 DT A 8 O4' - C1' - N1 ANGL. DEV. = -5.6 DEGREES REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = -7.5 DEGREES REMARK 500 DG A 10 C3' - C2' - C1' ANGL. DEV. = -7.2 DEGREES REMARK 500 DC A 11 O4' - C1' - N1 ANGL. DEV. = -5.3 DEGREES REMARK 500 DC B 1 N1 - C2 - O2 ANGL. DEV. = -3.9 DEGREES REMARK 500 DA B 6 O4' - C1' - N9 ANGL. DEV. = -5.8 DEGREES REMARK 500 DT B 8 O4' - C1' - N1 ANGL. DEV. = -6.7 DEGREES REMARK 500 DC B 9 N1 - C1' - C2' ANGL. DEV. = 8.5 DEGREES REMARK 500 DC B 9 O4' - C1' - N1 ANGL. DEV. = -7.3 DEGREES REMARK 500 DG B 10 C3' - C2' - C1' ANGL. DEV. = -5.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 4GLC A 1 12 PDB 4GLC 4GLC 1 12 DBREF 4GLC B 1 12 PDB 4GLC 4GLC 1 12 SEQRES 1 A 12 DC DG 5HC DG DA DA DT DT DC DG DC DG SEQRES 1 B 12 DC DG 5HC DG DA DA DT DT DC DG DC DG MODRES 4GLC 5HC A 3 DC MODRES 4GLC 5HC B 3 DC HET 5HC A 3 21 HET 5HC B 3 21 HETNAM 5HC 2'-DEOXY-5-(HYDROXYMETHYL)CYTIDINE 5'-(DIHYDROGEN HETNAM 2 5HC PHOSPHATE) FORMUL 1 5HC 2(C10 H16 N3 O8 P) FORMUL 3 HOH *40(H2 O) LINK O3' DG A 2 P 5HC A 3 1555 1555 1.61 LINK O3' 5HC A 3 P DG A 4 1555 1555 1.61 LINK O3' DG B 2 P 5HC B 3 1555 1555 1.62 LINK O3' 5HC B 3 P DG B 4 1555 1555 1.60 CRYST1 24.513 41.602 66.044 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 0.040795 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024037 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015141 0.00000