HEADER DNA 08-FEB-18 5ZAT TITLE CRYSTAL STRUCTURE OF 5-CARBOXYLCYTOSINE CONTAINING DECAMER DSDNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*CP*AP*GP*(CAC)P*GP*CP*TP*GP*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS CYTOSINE MODIFICATION, DNA EXPDTA X-RAY DIFFRACTION AUTHOR T.R.FU,L.ZHANG REVDAT 4 27-MAR-24 5ZAT 1 REMARK REVDAT 3 18-SEP-19 5ZAT 1 JRNL REVDAT 2 28-AUG-19 5ZAT 1 JRNL REVDAT 1 13-FEB-19 5ZAT 0 JRNL AUTH T.FU,L.LIU,Q.L.YANG,Y.WANG,P.XU,L.ZHANG,S.LIU,Q.DAI,Q.JI, JRNL AUTH 2 G.L.XU,C.HE,C.LUO,L.ZHANG JRNL TITL THYMINE DNA GLYCOSYLASE RECOGNIZES THE GEOMETRY ALTERATION JRNL TITL 2 OF MINOR GROOVES INDUCED BY 5-FORMYLCYTOSINE AND JRNL TITL 3 5-CARBOXYLCYTOSINE. JRNL REF CHEM SCI V. 10 7407 2019 JRNL REFN ISSN 2041-6520 JRNL PMID 31489163 JRNL DOI 10.1039/C9SC02807B REMARK 2 REMARK 2 RESOLUTION. 1.06 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.06 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 21376 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1096 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 29.7515 - 2.1190 0.94 2480 159 0.1668 0.1914 REMARK 3 2 2.1190 - 1.6820 0.98 2546 135 0.1606 0.1720 REMARK 3 3 1.6820 - 1.4694 0.97 2501 141 0.1554 0.1945 REMARK 3 4 1.4694 - 1.3350 1.00 2581 125 0.1544 0.1852 REMARK 3 5 1.3350 - 1.2393 0.98 2523 129 0.1476 0.1852 REMARK 3 6 1.2393 - 1.1663 0.99 2561 146 0.1381 0.1634 REMARK 3 7 1.1663 - 1.1078 0.99 2549 132 0.1394 0.1630 REMARK 3 8 1.1078 - 1.0596 0.98 2539 129 0.1356 0.1492 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.600 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) : 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 : 0.010 458 REMARK 3 ANGLE : 1.802 704 REMARK 3 CHIRALITY : 0.271 78 REMARK 3 PLANARITY : 0.018 22 REMARK 3 DIHEDRAL : 37.402 198 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 5ZAT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1300006773. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-16 REMARK 200 TEMPERATURE (KELVIN) : 180 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9676 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 300K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21838 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.060 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 (%) : 98.0 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.1200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.06 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.10 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM SODIUM SUCCINAT PH 5.5, 20MM REMARK 280 MGCL2, 0.5MM SPERMINE, 3.0 AMMONIUM SULFATE, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 18.16650 REMARK 290 SMTRY3 2 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: 1000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3820 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 154 O HOH A 164 2.02 REMARK 500 O HOH B 108 O HOH B 123 2.04 REMARK 500 O HOH A 170 O HOH B 156 2.04 REMARK 500 O HOH B 107 O HOH B 123 2.06 REMARK 500 O HOH B 127 O HOH B 165 2.06 REMARK 500 O HOH A 170 O HOH B 155 2.07 REMARK 500 O HOH B 151 O HOH B 165 2.07 REMARK 500 O HOH A 185 O HOH B 165 2.08 REMARK 500 O HOH A 161 O HOH A 178 2.08 REMARK 500 O HOH A 135 O HOH A 170 2.08 REMARK 500 O HOH A 179 O HOH B 153 2.09 REMARK 500 O HOH A 123 O HOH A 179 2.09 REMARK 500 O HOH A 170 O HOH B 160 2.11 REMARK 500 O HOH A 158 O HOH B 165 2.12 REMARK 500 O HOH A 122 O HOH A 179 2.12 REMARK 500 O HOH A 164 O HOH A 193 2.12 REMARK 500 O HOH A 159 O HOH A 170 2.13 REMARK 500 O HOH B 115 O HOH B 139 2.14 REMARK 500 O HOH A 104 O HOH B 166 2.16 REMARK 500 O HOH A 170 O HOH A 174 2.16 REMARK 500 O HOH A 150 O HOH B 115 2.18 REMARK 500 O HOH A 178 O HOH A 192 2.18 REMARK 500 O HOH A 110 O HOH B 163 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 178 O HOH B 107 2355 2.02 REMARK 500 O HOH B 111 O HOH B 165 1554 2.05 REMARK 500 O HOH A 164 O HOH B 128 2244 2.06 REMARK 500 O HOH A 137 O HOH A 179 1655 2.08 REMARK 500 O HOH A 112 O HOH A 178 2345 2.10 REMARK 500 O HOH B 125 O HOH B 165 1554 2.13 REMARK 500 O HOH A 164 O HOH B 139 2244 2.14 REMARK 500 O HOH A 111 O HOH A 183 2254 2.15 REMARK 500 O HOH A 179 O HOH A 180 1455 2.16 REMARK 500 O HOH A 150 O HOH A 164 2254 2.16 REMARK 500 O HOH A 161 O HOH B 123 2355 2.19 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 A 194 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH A 195 DISTANCE = 6.55 ANGSTROMS REMARK 525 HOH B 178 DISTANCE = 6.34 ANGSTROMS REMARK 525 HOH B 179 DISTANCE = 7.45 ANGSTROMS DBREF 5ZAT A 1 10 PDB 5ZAT 5ZAT 1 10 DBREF 5ZAT B 1 10 PDB 5ZAT 5ZAT 1 10 SEQRES 1 A 10 DC DC DA DG 1CC DG DC DT DG DG SEQRES 1 B 10 DC DC DA DG 1CC DG DC DT DG DG HET 1CC A 5 22 HET 1CC B 5 22 HETNAM 1CC 5-CARBOXY-2'-DEOXYCYTIDINE MONOPHOSPHATE FORMUL 1 1CC 2(C10 H14 N3 O9 P) FORMUL 3 HOH *174(H2 O) LINK O3' DG A 4 P 1CC A 5 1555 1555 1.61 LINK O3' 1CC A 5 P DG A 6 1555 1555 1.61 LINK O3' DG B 4 P 1CC B 5 1555 1555 1.61 LINK O3' 1CC B 5 P DG B 6 1555 1555 1.59 CRYST1 22.465 36.333 30.215 90.00 100.17 90.00 P 1 21 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 0.044514 0.000000 0.007989 0.00000 SCALE2 0.000000 0.027523 0.000000 0.00000 SCALE3 0.000000 0.000000 0.033625 0.00000