HEADER DNA 15-DEC-22 8FHX TITLE STRUCTURE OF LETTUCE APTAMER BOUND TO DFHBI-1T COMPND MOL_ID: 1; COMPND 2 MOLECULE: LETTUCE DNA APTAMER; 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, APTAMER, FLUORESCENCE, TURN-ON, FLUOROGENIC, FLUOROPHORE, G- KEYWDS 2 QUARTET, G-QUADRUPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.F.M.PASSALACQUA,A.R.FERRE-D'AMARE REVDAT 3 25-OCT-23 8FHX 1 REMARK REVDAT 2 05-JUL-23 8FHX 1 JRNL REVDAT 1 10-MAY-23 8FHX 0 JRNL AUTH L.F.M.PASSALACQUA,M.T.BANCO,J.D.MOON,X.LI,S.R.JAFFREY, JRNL AUTH 2 A.R.FERRE-D'AMARE JRNL TITL INTRICATE 3D ARCHITECTURE OF A DNA MIMIC OF GFP. JRNL REF NATURE V. 618 1078 2023 JRNL REFN ESSN 1476-4687 JRNL PMID 37344591 JRNL DOI 10.1038/S41586-023-06229-8 REMARK 2 REMARK 2 RESOLUTION. 2.50 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.440 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 4869 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.910 REMARK 3 FREE R VALUE TEST SET COUNT : 480 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 41.6100 - 3.6100 0.98 1543 166 0.1921 0.2361 REMARK 3 2 3.6100 - 2.8600 0.94 1395 155 0.2456 0.2744 REMARK 3 3 2.8600 - 2.5000 0.99 1425 159 0.3447 0.3990 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) : 0.417 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.572 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 54.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.34 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 : 0.005 1321 REMARK 3 ANGLE : 0.775 2046 REMARK 3 CHIRALITY : 0.036 222 REMARK 3 PLANARITY : 0.005 57 REMARK 3 DIHEDRAL : 35.863 564 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): -18.8767 -40.8021-102.2546 REMARK 3 T TENSOR REMARK 3 T11: 0.4293 T22: 0.6024 REMARK 3 T33: 0.2328 T12: -0.0298 REMARK 3 T13: -0.0526 T23: 0.0127 REMARK 3 L TENSOR REMARK 3 L11: 1.5277 L22: 5.5852 REMARK 3 L33: 6.4226 L12: 0.9526 REMARK 3 L13: 0.5818 L23: 2.1664 REMARK 3 S TENSOR REMARK 3 S11: 0.0040 S12: 0.3016 S13: 0.0311 REMARK 3 S21: -0.4752 S22: 0.2939 S23: 0.1949 REMARK 3 S31: -0.2567 S32: -0.1236 S33: -0.0924 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 8FHX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1000270808. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-APR-22 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 : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.912 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4870 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 59.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 10.20 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.28700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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: 8FHV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M MAGNESIUM CHLORIDE HEXAHYDRATE, REMARK 280 0.1 M HEPES PH 7.5, 30% (V/V) POLYETHYLENE GLYCOL MONOETHYL REMARK 280 ETHER 550, VAPOR DIFFUSION, SITTING DROP, 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 12.50750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.46050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.20850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.46050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.50750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.20850 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 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 DC A 38 N1 C2 O2 N3 C4 N4 C5 REMARK 470 DC A 38 C6 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 17 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 101 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 9 O6 REMARK 620 2 DG A 10 O6 77.9 REMARK 620 3 DG A 18 O6 125.8 66.8 REMARK 620 4 DG A 19 O6 71.1 88.3 68.2 REMARK 620 5 DG A 24 O6 106.8 167.3 101.6 82.3 REMARK 620 6 DG A 25 O6 163.8 106.9 69.4 123.8 71.9 REMARK 620 7 DG A 45 O6 96.1 67.8 106.2 155.1 122.4 72.3 REMARK 620 8 DG A 46 O6 66.8 125.7 165.9 115.5 66.5 98.8 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 10 O6 REMARK 620 2 DG A 18 O6 67.0 REMARK 620 3 DG A 25 O6 104.8 70.9 REMARK 620 4 DG A 45 O6 68.5 112.4 74.7 REMARK 620 5 2ZY A 107 O9 100.0 72.0 121.6 162.9 REMARK 620 6 HOH A 214 O 153.1 137.4 80.0 88.0 99.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 104 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT A 15 OP2 REMARK 620 2 HOH A 204 O 70.2 REMARK 620 3 HOH A 207 O 139.2 69.0 REMARK 620 4 HOH A 208 O 105.8 163.2 113.0 REMARK 620 5 HOH A 213 O 92.4 65.0 69.8 99.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 103 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC A 20 OP2 REMARK 620 2 HOH A 201 O 65.0 REMARK 620 3 HOH A 205 O 77.1 79.4 REMARK 620 4 HOH A 206 O 153.2 90.5 110.1 REMARK 620 5 HOH A 211 O 86.6 75.6 154.3 76.5 REMARK 620 6 HOH A 212 O 89.3 146.7 116.7 108.7 82.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 106 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC A 20 O2 REMARK 620 2 HOH A 209 O 68.2 REMARK 620 3 HOH A 216 O 98.9 150.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 105 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA A 52 OP2 REMARK 620 2 HOH A 202 O 57.5 REMARK 620 3 HOH A 217 O 107.4 155.1 REMARK 620 N 1 2 DBREF 8FHX A 1 53 PDB 8FHX 8FHX 1 53 SEQRES 1 A 53 DC DT DT DA DG DT DA DG DG DG DA DT DG SEQRES 2 A 53 DA DT DG DC DG DG DC DA DG DT DG DG DG SEQRES 3 A 53 DC DT DT DC DG DC DA DG DT DT DC DC DT SEQRES 4 A 53 DG DC DG DA DG DG DG DG DA DC DT DA DA SEQRES 5 A 53 DG HET K A 101 1 HET K A 102 1 HET MG A 103 1 HET MG A 104 1 HET MG A 105 1 HET MG A 106 1 HET 2ZY A 107 22 HETNAM K POTASSIUM ION HETNAM MG MAGNESIUM ION HETNAM 2ZY (5Z)-5-(3,5-DIFLUORO-4-HYDROXYBENZYLIDENE)-2-METHYL-3- HETNAM 2 2ZY (2,2,2-TRIFLUOROETHYL)-3,5-DIHYDRO-4H-IMIDAZOL-4-ONE FORMUL 2 K 2(K 1+) FORMUL 4 MG 4(MG 2+) FORMUL 8 2ZY C13 H9 F5 N2 O2 FORMUL 9 HOH *17(H2 O) LINK O6 DG A 9 K K A 101 1555 1555 2.79 LINK O6 DG A 10 K K A 101 1555 1555 2.73 LINK O6 DG A 10 K K A 102 1555 1555 2.82 LINK OP2 DT A 15 MG MG A 104 1555 1555 2.05 LINK O6 DG A 18 K K A 101 1555 1555 3.07 LINK O6 DG A 18 K K A 102 1555 1555 2.99 LINK O6 DG A 19 K K A 101 1555 1555 2.78 LINK OP2 DC A 20 MG MG A 103 1555 1555 2.01 LINK O2 DC A 20 MG MG A 106 1555 1555 2.59 LINK O6 DG A 24 K K A 101 1555 1555 2.77 LINK O6 DG A 25 K K A 101 1555 1555 2.79 LINK O6 DG A 25 K K A 102 1555 1555 2.78 LINK O6 DG A 45 K K A 101 1555 1555 2.85 LINK O6 DG A 45 K K A 102 1555 1555 2.71 LINK O6 DG A 46 K K A 101 1555 1555 3.10 LINK OP2 DA A 52 MG MG A 105 1555 1555 2.57 LINK K K A 102 O9 2ZY A 107 1555 1555 2.64 LINK K K A 102 O HOH A 214 1555 1555 2.90 LINK MG MG A 103 O HOH A 201 1555 1555 2.10 LINK MG MG A 103 O HOH A 205 1555 1555 2.01 LINK MG MG A 103 O HOH A 206 1555 1555 2.32 LINK MG MG A 103 O HOH A 211 1555 1555 2.06 LINK MG MG A 103 O HOH A 212 1555 1555 2.04 LINK MG MG A 104 O HOH A 204 1555 1555 2.16 LINK MG MG A 104 O HOH A 207 1555 1555 2.10 LINK MG MG A 104 O HOH A 208 1555 1555 2.15 LINK MG MG A 104 O HOH A 213 1555 1555 2.12 LINK MG MG A 105 O HOH A 202 1555 1555 1.95 LINK MG MG A 105 O HOH A 217 1555 1555 1.90 LINK MG MG A 106 O HOH A 209 1555 1555 2.12 LINK MG MG A 106 O HOH A 216 1555 1555 2.01 CRYST1 25.015 44.417 118.921 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 0.039976 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022514 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008409 0.00000