HEADER DNA 30-APR-25 9URS TITLE CRYSTAL STRUCTURE OF ADE1301 DNA APTAMER (ONE STRAND) BOUND TO TITLE 2 ADENOSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (39-MER); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS ADENOSINE/ATP DNA APTAMER, ADO, DNA EXPDTA X-RAY DIFFRACTION AUTHOR Y.LUO,X.CHEN,Y.REN,L.HUANG REVDAT 1 04-NOV-26 9URS 0 JRNL AUTH X.CHEN,Y.LUO,Y.REN,L.HUANG JRNL TITL CRYSTAL STRUCTURE OF ADENOSINE AND ATP-BINDING DNA APTAMER JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 2.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 5424 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.238 REMARK 3 R VALUE (WORKING SET) : 0.237 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 279 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 26.7100 - 3.6900 0.99 2664 146 0.2189 0.2348 REMARK 3 2 3.6900 - 2.9300 0.97 2481 133 0.3017 0.3283 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.298 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.445 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 93.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 90.77 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 1842 REMARK 3 ANGLE : 0.844 2838 REMARK 3 CHIRALITY : 0.046 314 REMARK 3 PLANARITY : 0.006 80 REMARK 3 DIHEDRAL : 35.379 768 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): 7.9403 -31.2283 -12.3440 REMARK 3 T TENSOR REMARK 3 T11: 0.7641 T22: 0.6972 REMARK 3 T33: 0.7743 T12: -0.1153 REMARK 3 T13: -0.1139 T23: 0.0758 REMARK 3 L TENSOR REMARK 3 L11: 0.7709 L22: 3.4797 REMARK 3 L33: 0.6950 L12: 0.1820 REMARK 3 L13: -0.2631 L23: 0.3451 REMARK 3 S TENSOR REMARK 3 S11: 0.1965 S12: -0.0320 S13: 0.1624 REMARK 3 S21: 0.5495 S22: -0.2106 S23: -0.2964 REMARK 3 S31: 0.1681 S32: -0.1120 S33: 0.0482 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : ens_1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : chain "A" REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : chain "B" REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9URS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 02-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1300058986. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-OCT-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL10U2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979183 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5480 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.930 REMARK 200 RESOLUTION RANGE LOW (A) : 50.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 11.20 REMARK 200 R MERGE (I) : 0.12700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.01 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.58300 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M CALCIUM CHLORIDE DIHYDRATE 0.1 REMARK 280 M BIS-TRIS PH 6.5 30% W/V POLYETHYLENE GLYCOL MONOMETHYL ETHER REMARK 280 550 20% W/V BENZAMIDINE HCL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K 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 25.15500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.12500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.52500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.12500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.15500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.52500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 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 DG A 13 C2' REMARK 470 DG B 13 C2' 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 O2 DT A 22 N2 DG A 25 2.03 REMARK 500 O2 DT B 22 N2 DG B 25 2.10 REMARK 500 REMARK 500 REMARK: NULL 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 16 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG A 18 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DT A 24 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG A 25 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 DG A 25 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG A 30 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT B 8 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DT B 24 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG B 25 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 9URS A 1 39 PDB 9URS 9URS 1 39 DBREF 9URS B 1 39 PDB 9URS 9URS 1 39 SEQRES 1 A 39 DG DA DC DG DA DC DG DT DT DT DG DC DG SEQRES 2 A 39 DA DT DG DA DG DA DA DC DT DT DT DG DG SEQRES 3 A 39 DT DT DC DG DA DA DG DG DT DC DG DT DC SEQRES 1 B 39 DG DA DC DG DA DC DG DT DT DT DG DC DG SEQRES 2 B 39 DA DT DG DA DG DA DA DC DT DT DT DG DG SEQRES 3 B 39 DT DT DC DG DA DA DG DG DT DC DG DT DC HET ADN A 101 19 HET ADN B 101 19 HET NA B 102 1 HET NA B 103 1 HETNAM ADN ADENOSINE HETNAM NA SODIUM ION FORMUL 3 ADN 2(C10 H13 N5 O4) FORMUL 5 NA 2(NA 1+) LINK O4 DT B 8 NA NA B 102 1555 1555 2.29 CRYST1 50.310 63.050 76.250 90.00 90.00 90.00 P 21 21 21 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 0.019877 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015860 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013115 0.00000 MTRIX1 1 -0.135739 0.118645 0.983615 23.50930 1 MTRIX2 1 -0.087695 -0.990346 0.107355 -61.59260 1 MTRIX3 1 0.986856 -0.071686 0.144833 -21.14746 1 CONECT 964 1647 CONECT 1609 1610 CONECT 1610 1609 1611 CONECT 1611 1610 1612 1613 CONECT 1612 1611 1617 CONECT 1613 1611 1614 1615 CONECT 1614 1613 CONECT 1615 1613 1616 1617 CONECT 1616 1615 CONECT 1617 1612 1615 1618 CONECT 1618 1617 1619 1627 CONECT 1619 1618 1620 CONECT 1620 1619 1621 CONECT 1621 1620 1622 1627 CONECT 1622 1621 1623 1624 CONECT 1623 1622 CONECT 1624 1622 1625 CONECT 1625 1624 1626 CONECT 1626 1625 1627 CONECT 1627 1618 1621 1626 CONECT 1628 1629 CONECT 1629 1628 1630 CONECT 1630 1629 1631 1632 CONECT 1631 1630 1636 CONECT 1632 1630 1633 1634 CONECT 1633 1632 CONECT 1634 1632 1635 1636 CONECT 1635 1634 CONECT 1636 1631 1634 1637 CONECT 1637 1636 1638 1646 CONECT 1638 1637 1639 CONECT 1639 1638 1640 CONECT 1640 1639 1641 1646 CONECT 1641 1640 1642 1643 CONECT 1642 1641 CONECT 1643 1641 1644 CONECT 1644 1643 1645 CONECT 1645 1644 1646 CONECT 1646 1637 1640 1645 CONECT 1647 964 MASTER 267 0 4 0 0 0 0 9 1646 2 40 6 END