HEADER DNA 08-APR-22 7XHD TITLE CRYSTAL STRUCTURE OF A DIMERIC INTERLOCKED PARALLEL G-QUADRUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*TP*GP*GP*GP*T)- COMPND 3 3'); COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS G-QUADRUPLEX, INTERLOCKED, DNA EXPDTA X-RAY DIFFRACTION AUTHOR K.H.NGO,C.W.LIEW,S.LATTMANN,F.R.WINNERDY,A.T.PHAN REVDAT 2 29-NOV-23 7XHD 1 REMARK REVDAT 1 15-FEB-23 7XHD 0 JRNL AUTH K.H.NGO,C.W.LIEW,S.LATTMANN,F.R.WINNERDY,A.T.PHAN JRNL TITL CRYSTAL STRUCTURES OF AN HIV-1 INTEGRASE APTAMER: FORMATION JRNL TITL 2 OF A WATER-MEDIATED A•G•G•G•G PENTAD JRNL TITL 3 IN AN INTERLOCKED G-QUADRUPLEX. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 613 153 2022 JRNL REFN ESSN 1090-2104 JRNL PMID 35561583 JRNL DOI 10.1016/J.BBRC.2022.04.020 REMARK 2 REMARK 2 RESOLUTION. 1.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 11627 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1172 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 24.5400 - 3.3200 0.98 1331 146 0.1345 0.1510 REMARK 3 2 3.3200 - 2.6400 0.97 1308 154 0.2152 0.2594 REMARK 3 3 2.6300 - 2.3000 0.97 1347 146 0.2019 0.2191 REMARK 3 4 2.3000 - 2.0900 0.97 1304 146 0.2063 0.2433 REMARK 3 5 2.0900 - 1.9400 0.97 1317 147 0.1967 0.2492 REMARK 3 6 1.9400 - 1.8300 0.96 1293 144 0.2046 0.2401 REMARK 3 7 1.8300 - 1.7400 0.96 1299 147 0.2304 0.2469 REMARK 3 8 1.7400 - 1.6600 0.92 1256 142 0.2241 0.2460 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) : 0.149 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.300 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.13 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.89 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 : 0.008 768 REMARK 3 ANGLE : 0.980 1192 REMARK 3 CHIRALITY : 0.046 126 REMARK 3 PLANARITY : 0.009 32 REMARK 3 DIHEDRAL : 31.893 312 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -0.6145 -2.6700 14.6701 REMARK 3 T TENSOR REMARK 3 T11: 0.2356 T22: 0.2340 REMARK 3 T33: 0.2239 T12: -0.0047 REMARK 3 T13: 0.0016 T23: 0.0141 REMARK 3 L TENSOR REMARK 3 L11: 0.7587 L22: 0.4593 REMARK 3 L33: 0.4187 L12: -0.4483 REMARK 3 L13: -0.1523 L23: -0.1543 REMARK 3 S TENSOR REMARK 3 S11: -0.0392 S12: 0.0309 S13: -0.0276 REMARK 3 S21: 0.0135 S22: 0.0121 S23: -0.0370 REMARK 3 S31: 0.0394 S32: -0.0128 S33: -0.0001 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 7XHD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-APR-22. REMARK 100 THE DEPOSITION ID IS D_1300028822. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAR-22 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.953659 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11663 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 24.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.7600 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) : 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 1.19.2_4158 REMARK 200 STARTING MODEL: 7XDH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.002 M COPPER(II) CHLORIDE DIHYDRATE, REMARK 280 0.05 M TRIS HYDROCHLORIDE PH 8.5, 1.8 M LITHIUM SULFATE REMARK 280 MONOHYDRATE, 0.0005 M SPERMINE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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, 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 1 O4' - C1' - N9 ANGL. DEV. = 2.0 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 A 247 DISTANCE = 5.85 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 K A 103 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 1 O6 REMARK 620 2 DG A 2 O6 73.6 REMARK 620 3 DG A 6 O6 108.4 70.9 REMARK 620 4 DG A 13 O6 113.9 71.2 110.0 REMARK 620 5 DG B 1 O6 178.3 106.5 70.1 67.6 REMARK 620 6 DG B 2 O6 105.6 177.6 111.5 107.3 74.4 REMARK 620 7 DG B 6 O6 70.1 111.8 69.0 175.8 108.4 69.8 REMARK 620 8 DG B 13 O6 68.7 106.4 176.7 70.3 112.8 71.2 110.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 101 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 1 O6 REMARK 620 2 DG B 2 O6 108.8 REMARK 620 3 DG B 3 O6 157.5 75.6 REMARK 620 4 DG B 6 O6 70.8 69.4 91.3 REMARK 620 5 DG B 7 O6 90.7 132.1 71.7 77.2 REMARK 620 6 DG B 10 O6 76.8 154.4 109.1 133.9 71.3 REMARK 620 7 DG B 13 O6 68.2 69.6 131.8 106.0 155.3 90.7 REMARK 620 8 DG B 14 O6 130.7 88.3 70.5 154.4 111.9 70.7 76.1 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 102 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 2 O6 REMARK 620 2 DG A 3 O6 76.8 REMARK 620 3 DG A 6 O6 69.1 88.5 REMARK 620 4 DG A 7 O6 134.5 70.5 79.2 REMARK 620 5 DG A 10 O6 153.7 109.3 135.0 69.4 REMARK 620 6 DG A 13 O6 71.3 136.0 106.8 151.8 88.8 REMARK 620 7 DG A 14 O6 90.2 71.4 154.3 107.6 68.8 79.2 REMARK 620 8 DG B 1 O6 106.8 152.7 68.6 90.2 79.8 67.8 134.5 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 101 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 3 O6 REMARK 620 2 DG A 4 O6 74.0 REMARK 620 3 DG A 7 O6 67.8 90.0 REMARK 620 4 DG A 8 O6 126.6 74.9 70.0 REMARK 620 5 DG A 10 O6 100.9 154.4 65.3 89.5 REMARK 620 6 DG A 11 O6 154.2 122.7 126.5 78.8 72.2 REMARK 620 7 DG A 14 O6 68.5 131.7 102.5 153.2 64.6 86.4 REMARK 620 8 DG A 15 O6 91.9 77.5 158.7 121.8 128.1 74.8 74.5 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 102 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 3 O6 REMARK 620 2 DG B 4 O6 73.1 REMARK 620 3 DG B 7 O6 66.8 90.7 REMARK 620 4 DG B 8 O6 130.5 76.9 75.2 REMARK 620 5 DG B 10 O6 102.2 155.7 66.1 89.6 REMARK 620 6 DG B 11 O6 152.7 121.2 130.6 76.9 73.8 REMARK 620 7 DG B 14 O6 66.2 128.7 100.3 154.4 66.0 88.2 REMARK 620 8 DG B 15 O6 87.8 74.7 153.7 120.8 129.5 75.5 73.9 REMARK 620 N 1 2 3 4 5 6 7 DBREF 7XHD A 1 16 PDB 7XHD 7XHD 1 16 DBREF 7XHD B 1 16 PDB 7XHD 7XHD 1 16 SEQRES 1 A 16 DG DG DG DG DT DG DG DG DT DG DG DT DG SEQRES 2 A 16 DG DG DT SEQRES 1 B 16 DG DG DG DG DT DG DG DG DT DG DG DT DG SEQRES 2 B 16 DG DG DT HET K A 101 1 HET K A 102 1 HET K A 103 1 HET K B 101 1 HET K B 102 1 HETNAM K POTASSIUM ION FORMUL 3 K 5(K 1+) FORMUL 8 HOH *99(H2 O) LINK O6 DG A 1 K K A 103 1555 1555 2.89 LINK O6 DG A 1 K K B 101 1555 1555 2.80 LINK O6 DG A 2 K K A 102 1555 1555 2.75 LINK O6 DG A 2 K K A 103 1555 1555 2.75 LINK O6 DG A 3 K K A 101 1555 1555 2.90 LINK O6 DG A 3 K K A 102 1555 1555 2.80 LINK O6 DG A 4 K K A 101 1555 1555 2.72 LINK O6 DG A 6 K K A 102 1555 1555 2.90 LINK O6 DG A 6 K K A 103 1555 1555 2.78 LINK O6 DG A 7 K K A 101 1555 1555 2.91 LINK O6 DG A 7 K K A 102 1555 1555 2.82 LINK O6 DG A 8 K K A 101 1555 1555 2.73 LINK O6 DG A 10 K K A 101 1555 1555 2.94 LINK O6 DG A 10 K K A 102 1555 1555 2.73 LINK O6 DG A 11 K K A 101 1555 1555 2.68 LINK O6 DG A 13 K K A 102 1555 1555 2.86 LINK O6 DG A 13 K K A 103 1555 1555 2.87 LINK O6 DG A 14 K K A 101 1555 1555 2.88 LINK O6 DG A 14 K K A 102 1555 1555 2.78 LINK O6 DG A 15 K K A 101 1555 1555 2.76 LINK K K A 102 O6 DG B 1 1555 1555 2.82 LINK K K A 103 O6 DG B 1 1555 1555 2.83 LINK K K A 103 O6 DG B 2 1555 1555 2.80 LINK K K A 103 O6 DG B 6 1555 1555 2.85 LINK K K A 103 O6 DG B 13 1555 1555 2.79 LINK O6 DG B 2 K K B 101 1555 1555 2.78 LINK O6 DG B 3 K K B 101 1555 1555 2.77 LINK O6 DG B 3 K K B 102 1555 1555 2.88 LINK O6 DG B 4 K K B 102 1555 1555 2.74 LINK O6 DG B 6 K K B 101 1555 1555 2.89 LINK O6 DG B 7 K K B 101 1555 1555 2.73 LINK O6 DG B 7 K K B 102 1555 1555 2.96 LINK O6 DG B 8 K K B 102 1555 1555 2.72 LINK O6 DG B 10 K K B 101 1555 1555 2.74 LINK O6 DG B 10 K K B 102 1555 1555 2.89 LINK O6 DG B 11 K K B 102 1555 1555 2.70 LINK O6 DG B 13 K K B 101 1555 1555 2.92 LINK O6 DG B 14 K K B 101 1555 1555 2.72 LINK O6 DG B 14 K K B 102 1555 1555 2.92 LINK O6 DG B 15 K K B 102 1555 1555 2.72 CRYST1 29.403 30.917 31.584 98.19 97.15 109.13 P 1 2 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 0.034010 0.011794 0.006700 0.00000 SCALE2 0.000000 0.034234 0.006820 0.00000 SCALE3 0.000000 0.000000 0.032537 0.00000