HEADER DNA 17-SEP-13 4C63 TITLE ULTRA HIGH RESOLUTION DICKERSON-DREW DODECAMER B-DNA WITH 5- TITLE 2 METHYLCYSTOSINE MODIFICATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*5CMP*GP*CP*GP)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: 5-METHYL CYTOSINE AT POSITION C9 STRAND A AND C21 COMPND 6 STRAND B, DICKERSON-DREW SEQUENCE DODECAMER SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS DNA, CYTOSINE MODIFICATION EXPDTA X-RAY DIFFRACTION AUTHOR M.MCDONOUGH,A.H.EL-SAGHEER,T.BROWN,C.J.SCHOFIELD REVDAT 6 20-DEC-23 4C63 1 REMARK LINK REVDAT 5 21-FEB-18 4C63 1 JRNL REVDAT 4 07-MAY-14 4C63 1 SEQRES REVDAT 3 12-FEB-14 4C63 1 JRNL DBREF REVDAT 2 11-DEC-13 4C63 1 JRNL REVDAT 1 02-OCT-13 4C63 0 JRNL AUTH L.LERCHER,M.A.MCDONOUGH,A.H.EL-SAGHEER,A.THALHAMMER, JRNL AUTH 2 S.KRIAUCIONIS,T.BROWN,C.J.SCHOFIELD JRNL TITL STRUCTURAL INSIGHTS INTO HOW 5-HYDROXYMETHYLATION INFLUENCES JRNL TITL 2 TRANSCRIPTION FACTOR BINDING. JRNL REF CHEM. COMMUN. (CAMB.) V. 50 1794 2014 JRNL REFN ESSN 1364-548X JRNL PMID 24287551 JRNL DOI 10.1039/C3CC48151D REMARK 2 REMARK 2 RESOLUTION. 1.32 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.32 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 15039 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1503 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 25.3400 - 2.9344 0.97 1360 151 0.1527 0.1554 REMARK 3 2 2.9344 - 2.3296 0.99 1301 146 0.1731 0.2427 REMARK 3 3 2.3296 - 2.0353 0.99 1277 140 0.1500 0.2021 REMARK 3 4 2.0353 - 1.8493 0.99 1283 144 0.1419 0.1721 REMARK 3 5 1.8493 - 1.7168 0.99 1266 141 0.1096 0.1680 REMARK 3 6 1.7168 - 1.6156 0.98 1249 135 0.1001 0.1565 REMARK 3 7 1.6156 - 1.5347 0.97 1234 138 0.1130 0.2065 REMARK 3 8 1.5347 - 1.4679 0.93 1165 134 0.1396 0.1949 REMARK 3 9 1.4679 - 1.4114 0.93 1186 130 0.1629 0.2200 REMARK 3 10 1.4114 - 1.3627 0.90 1129 127 0.1919 0.2955 REMARK 3 11 1.3627 - 1.3201 0.85 1086 117 0.2250 0.2821 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.50 REMARK 3 SHRINKAGE RADIUS : 0.29 REMARK 3 K_SOL : 0.51 REMARK 3 B_SOL : 57.41 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.89620 REMARK 3 B22 (A**2) : -1.81270 REMARK 3 B33 (A**2) : -1.08350 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 : 0.021 552 REMARK 3 ANGLE : 2.364 855 REMARK 3 CHIRALITY : 0.113 92 REMARK 3 PLANARITY : 0.033 24 REMARK 3 DIHEDRAL : 31.124 224 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 4C63 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1290058374. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-AUG-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.917300 REMARK 200 MONOCHROMATOR : SI (111) DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS 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 : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16355 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 25.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 12.40 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.9 REMARK 200 DATA REDUNDANCY IN SHELL : 12.40 REMARK 200 R MERGE FOR SHELL (I) : 1.23000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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 1BNA REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% MPD, SPERMINE, MAGNESIUM CHLORIDE, REMARK 280 SODIUM CACODYLATE PH 7.5 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 12.22800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.70700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.03000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.70700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.22800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.03000 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: 2440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.6 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 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 DA A 5 C8 DA A 5 N9 -0.049 REMARK 500 DG B 14 O3' DG B 14 C3' -0.069 REMARK 500 DC B 15 O3' DC B 15 C3' -0.051 REMARK 500 DC B 23 O3' DC B 23 C3' -0.050 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 3 C6 - N1 - C2 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = -5.6 DEGREES REMARK 500 DA A 6 C5 - C6 - N1 ANGL. DEV. = -3.1 DEGREES REMARK 500 DG A 10 O5' - P - OP2 ANGL. DEV. = -7.3 DEGREES REMARK 500 DG A 10 C3' - C2' - C1' ANGL. DEV. = -6.8 DEGREES REMARK 500 DG A 12 C4 - C5 - N7 ANGL. DEV. = -2.5 DEGREES REMARK 500 DG B 14 O4' - C4' - C3' ANGL. DEV. = 6.9 DEGREES REMARK 500 DG B 14 C1' - O4' - C4' ANGL. DEV. = -9.3 DEGREES REMARK 500 DG B 14 O4' - C1' - N9 ANGL. DEV. = -6.4 DEGREES REMARK 500 DG B 16 N9 - C4 - C5 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA B 17 N1 - C2 - N3 ANGL. DEV. = -4.0 DEGREES REMARK 500 DA B 17 C8 - N9 - C4 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA B 18 O4' - C1' - N9 ANGL. DEV. = -4.2 DEGREES REMARK 500 DT B 20 O4' - C1' - N1 ANGL. DEV. = -5.0 DEGREES REMARK 500 DT B 20 C4 - C5 - C7 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG B 22 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DG B 22 C5 - C6 - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 DC B 23 O4' - C4' - C3' ANGL. DEV. = 6.5 DEGREES REMARK 500 DC B 23 C1' - O4' - C4' ANGL. DEV. = -8.0 DEGREES REMARK 500 DC B 23 O4' - C1' - N1 ANGL. DEV. = -5.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2051 DISTANCE = 5.89 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 100 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2004 O REMARK 620 2 HOH A2013 O 90.7 REMARK 620 3 HOH A2019 O 87.5 92.3 REMARK 620 4 HOH A2058 O 87.9 174.6 92.8 REMARK 620 5 HOH A2059 O 94.5 88.3 177.9 86.6 REMARK 620 6 HOH A2060 O 174.3 89.6 86.8 92.4 91.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 100 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4C5X RELATED DB: PDB REMARK 900 ULTRA HIGH RESOLUTION DICKERSON-DREW DODECAMER B-DNA WITH 5- REMARK 900 HYDROXYMETHYL-CYTOSINE MODIFICATION REMARK 900 RELATED ID: 4C64 RELATED DB: PDB REMARK 900 ULTRA HIGH RESOLUTION DICKERSON-DREW DODECAMER B-DNA DBREF 4C63 A 1 12 PDB 4C63 4C63 1 12 DBREF 4C63 B 13 24 PDB 4C63 4C63 13 24 SEQRES 1 A 12 DC DG DC DG DA DA DT DT 5CM DG DC DG SEQRES 1 B 12 DC DG DC DG DA DA DT DT 5CM DG DC DG MODRES 4C63 5CM A 9 DC MODRES 4C63 5CM B 21 DC HET 5CM A 9 20 HET 5CM B 21 20 HET MG A 100 1 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 1 5CM 2(C10 H16 N3 O7 P) FORMUL 3 MG MG 2+ FORMUL 4 HOH *94(H2 O) LINK O3' DT A 8 P 5CM A 9 1555 1555 1.64 LINK O3' 5CM A 9 P DG A 10 1555 1555 1.62 LINK O3' DT B 20 P 5CM B 21 1555 1555 1.61 LINK O3' 5CM B 21 P DG B 22 1555 1555 1.62 LINK MG MG A 100 O HOH A2004 1555 1555 2.06 LINK MG MG A 100 O HOH A2013 1555 1555 2.07 LINK MG MG A 100 O HOH A2019 1555 1555 2.04 LINK MG MG A 100 O HOH A2058 1555 1555 2.07 LINK MG MG A 100 O HOH A2059 1555 1555 2.06 LINK MG MG A 100 O HOH A2060 1555 1555 2.07 SITE 1 AC1 6 HOH A2004 HOH A2013 HOH A2019 HOH A2058 SITE 2 AC1 6 HOH A2059 HOH A2060 CRYST1 24.456 40.060 65.414 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 0.040890 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024963 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015287 0.00000