HEADER DNA 03-JUL-18 6GZ6 TITLE STRUCTURE OF A LEFT-HANDED G-QUADRUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (27-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS G-QUADRUPLEX, DNA EXPDTA X-RAY DIFFRACTION AUTHOR B.BAKALAR,B.HEDDI,E.SCHMITT,Y.MECHULAM,A.T.PHAN REVDAT 2 17-JAN-24 6GZ6 1 LINK REVDAT 1 24-APR-19 6GZ6 0 JRNL AUTH B.BAKALAR,B.HEDDI,E.SCHMITT,Y.MECHULAM,A.T.PHAN JRNL TITL A MINIMAL SEQUENCE FOR LEFT-HANDED G-QUADRUPLEX FORMATION. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 58 2331 2019 JRNL REFN ESSN 1521-3773 JRNL PMID 30481397 JRNL DOI 10.1002/ANIE.201812628 REMARK 2 REMARK 2 RESOLUTION. 2.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 4285 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.640 REMARK 3 FREE R VALUE TEST SET COUNT : 199 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 30.9290 - 2.0062 0.98 4086 199 0.1849 0.2308 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) : 0.060 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.780 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 : 0.008 638 REMARK 3 ANGLE : 0.997 990 REMARK 3 CHIRALITY : 0.049 107 REMARK 3 PLANARITY : 0.010 27 REMARK 3 DIHEDRAL : 38.396 266 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 6GZ6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1200010765. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 12.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999996 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4341 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 31.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 13.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.6 REMARK 200 DATA REDUNDANCY IN SHELL : 13.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.66800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.950 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: 4M5U REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% MPD, 12MM SPERMINE, 80MM KCL, 20MM REMARK 280 BACL2, 40MM NACACODYLATE PH7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 294K 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 14.78500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.14000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.81500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.14000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.78500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.81500 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 KCAL/MOL 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 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 102 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 1 O6 REMARK 620 2 DG A 3 O6 94.3 REMARK 620 3 DG A 4 O6 70.6 79.8 REMARK 620 4 DG A 6 O6 156.4 67.7 90.5 REMARK 620 5 DG A 7 O6 104.7 130.2 64.7 78.3 REMARK 620 6 DG A 9 O6 134.1 105.5 152.6 67.9 93.5 REMARK 620 7 DG A 10 O6 69.4 159.6 104.9 131.2 68.0 79.7 REMARK 620 8 DG A 12 O6 78.2 68.4 133.1 107.1 160.0 71.8 95.5 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 103 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 1 O6 REMARK 620 2 DG A 4 O6 68.0 REMARK 620 3 DG A 7 O6 102.6 65.2 REMARK 620 4 DG A 10 O6 67.1 103.7 68.8 REMARK 620 5 DG A 15 O6 91.0 152.1 140.4 83.4 REMARK 620 6 DG A 18 O6 151.7 138.1 85.5 91.6 67.2 REMARK 620 7 DG A 21 O6 136.8 81.5 90.7 153.3 104.5 69.1 REMARK 620 8 DG A 24 O6 82.7 88.8 148.1 139.1 69.8 104.9 66.2 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 15 O6 REMARK 620 2 DG A 17 O6 92.6 REMARK 620 3 DG A 18 O6 67.3 78.0 REMARK 620 4 DG A 20 O6 152.9 68.5 89.3 REMARK 620 5 DG A 21 O6 102.3 130.8 65.8 78.4 REMARK 620 6 DG A 23 O6 133.8 109.5 155.1 72.6 93.3 REMARK 620 7 DG A 24 O6 70.9 161.0 102.9 130.2 64.2 77.8 REMARK 620 8 DG A 26 O6 74.8 73.6 130.9 115.4 155.5 73.4 92.5 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 103 DBREF 6GZ6 A 1 27 PDB 6GZ6 6GZ6 1 27 SEQRES 1 A 27 DG DT DG DG DT DG DG DT DG DG DT DG DT SEQRES 2 A 27 DT DG DT DG DG DT DG DG DT DG DG DT DG SEQRES 3 A 27 DT HET K A 101 1 HET K A 102 1 HET K A 103 1 HETNAM K POTASSIUM ION FORMUL 2 K 3(K 1+) FORMUL 5 HOH *10(H2 O) LINK O6 DG A 1 K K A 102 1555 1555 2.81 LINK O6 DG A 1 K K A 103 1555 1555 2.97 LINK O6 DG A 3 K K A 102 1555 1555 2.99 LINK O6 DG A 4 K K A 102 1555 1555 2.88 LINK O6 DG A 4 K K A 103 1555 1555 2.92 LINK O6 DG A 6 K K A 102 1555 1555 2.91 LINK O6 DG A 7 K K A 102 1555 1555 2.88 LINK O6 DG A 7 K K A 103 1555 1555 2.81 LINK O6 DG A 9 K K A 102 1555 1555 2.91 LINK O6 DG A 10 K K A 102 1555 1555 2.87 LINK O6 DG A 10 K K A 103 1555 1555 2.88 LINK O6 DG A 12 K K A 102 1555 1555 2.90 LINK O6 DG A 15 K K A 101 1555 1555 2.78 LINK O6 DG A 15 K K A 103 1555 1555 2.86 LINK O6 DG A 17 K K A 101 1555 1555 2.79 LINK O6 DG A 18 K K A 101 1555 1555 2.88 LINK O6 DG A 18 K K A 103 1555 1555 2.80 LINK O6 DG A 20 K K A 101 1555 1555 2.88 LINK O6 DG A 21 K K A 101 1555 1555 3.02 LINK O6 DG A 21 K K A 103 1555 1555 2.86 LINK O6 DG A 23 K K A 101 1555 1555 2.89 LINK O6 DG A 24 K K A 101 1555 1555 2.96 LINK O6 DG A 24 K K A 103 1555 1555 2.96 LINK O6 DG A 26 K K A 101 1555 1555 2.68 SITE 1 AC1 9 DG A 15 DG A 17 DG A 18 DG A 20 SITE 2 AC1 9 DG A 21 DG A 23 DG A 24 DG A 26 SITE 3 AC1 9 K A 103 SITE 1 AC2 9 DG A 1 DG A 3 DG A 4 DG A 6 SITE 2 AC2 9 DG A 7 DG A 9 DG A 10 DG A 12 SITE 3 AC2 9 K A 103 SITE 1 AC3 10 DG A 1 DG A 4 DG A 7 DG A 10 SITE 2 AC3 10 DG A 15 DG A 18 DG A 21 DG A 24 SITE 3 AC3 10 K A 101 K A 102 CRYST1 29.570 37.630 54.280 90.00 90.00 90.00 P 21 21 21 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 0.033818 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026575 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018423 0.00000