HEADER DNA 01-MAY-18 5ZT2 TITLE CRYSTAL STRUCTURE OF CCG DNA REPEATS AT 1.66 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*TP*CP*CP*GP*CP*CP*GP*CP*CP*GP*A)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS DNA STRUCTURES, I-MOTIFS, NEUROLOGICAL DISEASE, TETRAPLEX STRUCTURES, KEYWDS 2 DNA EXPDTA X-RAY DIFFRACTION AUTHOR M.H.HOU,P.C.WU,R.B.SATANGE,Y.W.CHEN REVDAT 3 27-MAR-24 5ZT2 1 LINK REVDAT 2 22-MAY-19 5ZT2 1 REMARK REVDAT 1 15-MAY-19 5ZT2 0 SPRSDE 15-MAY-19 5ZT2 4QNO JRNL AUTH M.H.HOU JRNL TITL CRYSTALLOGRAPHIC ANALYSIS OF CONFORMATIONAL CHANGE IN CCG JRNL TITL 2 REPEATS INTO I-MOTIF AND UNUSUAL DNA DUPLEX IN PRESENCE AND JRNL TITL 3 ABSENCE OF COII(CHRO)2 COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.W.CHEN,C.R.JHAN,S.NEIDLE,M.H.HOU REMARK 1 TITL STRUCTURAL BASIS FOR THE IDENTIFICATION OF AN I-MOTIF REMARK 1 TITL 2 TETRAPLEX CORE WITH A PARALLEL-DUPLEX JUNCTION AS A REMARK 1 TITL 3 STRUCTURAL MOTIF IN CCG TRIPLET REPEATS. REMARK 1 REF ANGEW.CHEM.INT.ED.ENGL. V. 53 10682 2014 REMARK 1 REFN ESSN 1521-3773 REMARK 1 PMID 25139267 REMARK 1 DOI 10.1002/ANIE.201405637 REMARK 2 REMARK 2 RESOLUTION. 1.66 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) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.005 REMARK 3 COMPLETENESS FOR RANGE (%) : 67.1 REMARK 3 NUMBER OF REFLECTIONS : 3447 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.009 REMARK 3 FREE R VALUE TEST SET COUNT : 345 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 12.4441 - 2.0898 0.71 1678 187 0.2188 0.2335 REMARK 3 2 1.7192 - 1.6600 0.63 1424 158 0.2802 0.3224 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) : 0.209 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.626 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.74 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 : 0.006 243 REMARK 3 ANGLE : 0.692 372 REMARK 3 CHIRALITY : 0.030 43 REMARK 3 PLANARITY : 0.003 11 REMARK 3 DIHEDRAL : 31.491 106 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 5ZT2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1300007600. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL15A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.60572, 1.56518, 1.60490 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3447 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 41.7240 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.66 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.72 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.27200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM SODIUM CACODYLATE, 1MM MAGNESIUM REMARK 280 CHLORIDE, 5% MPD, 2MM COBALT(II) CHLORIDE, 1MM CHROMOMYCIN A3, REMARK 280 PH 6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277.15K 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 27.16400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 19.14950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 19.14950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 40.74600 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 19.14950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 19.14950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 13.58200 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 19.14950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 19.14950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 40.74600 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 19.14950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 19.14950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 13.58200 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 27.16400 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 27.16400 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 220 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 244 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 257 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 259 LIES ON A SPECIAL POSITION. 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 251 O HOH A 253 1.68 REMARK 500 O HOH A 241 O HOH A 248 2.05 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 254 DISTANCE = 6.84 ANGSTROMS REMARK 525 HOH A 255 DISTANCE = 7.40 ANGSTROMS REMARK 525 HOH A 256 DISTANCE = 7.58 ANGSTROMS REMARK 525 HOH A 257 DISTANCE = 7.69 ANGSTROMS REMARK 525 HOH A 258 DISTANCE = 8.51 ANGSTROMS REMARK 525 HOH A 259 DISTANCE = 8.91 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 CO A 101 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 4 N7 REMARK 620 2 HOH A 216 O 98.1 REMARK 620 3 HOH A 226 O 93.2 166.2 REMARK 620 4 HOH A 228 O 83.9 87.5 85.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 102 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 7 N7 REMARK 620 2 HOH A 210 O 88.2 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO A 102 DBREF 5ZT2 A 1 11 PDB 5ZT2 5ZT2 1 11 SEQRES 1 A 11 DT DC DC DG DC DC DG DC DC DG DA HET CO A 101 1 HET CO A 102 1 HETNAM CO COBALT (II) ION FORMUL 2 CO 2(CO 2+) FORMUL 4 HOH *59(H2 O) LINK N7 DG A 4 CO CO A 101 1555 1555 2.35 LINK N7 DG A 7 CO CO A 102 1555 1555 2.58 LINK CO CO A 101 O HOH A 216 1555 1555 2.29 LINK CO CO A 101 O HOH A 226 1555 1555 1.96 LINK CO CO A 101 O HOH A 228 1555 1555 2.42 LINK CO CO A 102 O HOH A 210 1555 1555 2.68 SITE 1 AC1 5 DG A 4 DC A 5 HOH A 216 HOH A 226 SITE 2 AC1 5 HOH A 228 SITE 1 AC2 4 DC A 6 DG A 7 HOH A 210 HOH A 229 CRYST1 38.299 38.299 54.328 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 0.026110 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026110 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018407 0.00000