HEADER DNA 18-SEP-20 7D31 TITLE THE TBA-PB2+ COMPLEX IN P41212 SPACE GROUP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)- 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 QUADRUPLEX, PB2+-BINDING, DNA APTAMER, DNA EXPDTA X-RAY DIFFRACTION AUTHOR H.H.LIU,Y.Q.GAO,J.SHENG,J.H.GAN REVDAT 2 06-APR-22 7D31 1 JRNL REVDAT 1 22-SEP-21 7D31 0 JRNL AUTH H.LIU,Y.GAO,J.MATHIVANAN,F.SHEN,X.CHEN,Y.LI,Z.SHAO,Y.ZHANG, JRNL AUTH 2 Q.SHAO,J.SHENG,J.GAN JRNL TITL STRUCTURE-GUIDED DEVELOPMENT OF PB 2+ -BINDING DNA APTAMERS. JRNL REF SCI REP V. 12 460 2022 JRNL REFN ESSN 2045-2322 JRNL PMID 35013452 JRNL DOI 10.1038/S41598-021-04243-2 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.23 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 16540 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.127 REMARK 3 R VALUE (WORKING SET) : 0.126 REMARK 3 FREE R VALUE : 0.148 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 811 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 27.2250 - 2.5367 0.95 2731 142 0.1454 0.1657 REMARK 3 2 2.5367 - 2.0136 1.00 2673 145 0.1279 0.1434 REMARK 3 3 2.0136 - 1.7592 1.00 2654 139 0.0955 0.1155 REMARK 3 4 1.7592 - 1.5983 1.00 2630 127 0.0843 0.1118 REMARK 3 5 1.5983 - 1.4838 1.00 2609 130 0.1058 0.1409 REMARK 3 6 1.4838 - 1.3963 0.93 2432 128 0.1669 0.2100 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.91 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 : 0.007 706 REMARK 3 ANGLE : 0.997 1094 REMARK 3 CHIRALITY : 0.047 118 REMARK 3 PLANARITY : 0.009 30 REMARK 3 DIHEDRAL : 32.866 292 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 : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A REMARK 3 SELECTION : CHAIN B REMARK 3 ATOM PAIRS NUMBER : 292 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7D31 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1300018657. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-DEC-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16599 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.396 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 (%) : 97.9 REMARK 200 DATA REDUNDANCY : 14.40 REMARK 200 R MERGE (I) : 0.10900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.38100 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: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: BLOCK REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% V/V MPD, 40 MM SODIUM CACODYLATE REMARK 280 PH 7.0, 12 MM SPERMINE TETRA-HCL, AND 80 MM SODIUM CHLORIDE, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 49.94800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 20.00850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 20.00850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 24.97400 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 20.00850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 20.00850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 74.92200 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 20.00850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 20.00850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 24.97400 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 20.00850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 20.00850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 74.92200 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 49.94800 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 2 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG A 11 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DG B 11 O4' - C1' - N9 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 PB A 101 PB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 1 O6 REMARK 620 2 DG A 2 O6 69.6 REMARK 620 3 DG A 5 O6 118.6 73.3 REMARK 620 4 DG A 6 O6 71.2 98.1 67.6 REMARK 620 5 DG A 10 O6 112.8 167.5 95.5 72.1 REMARK 620 6 DG A 11 O6 167.6 111.6 72.8 120.0 68.9 REMARK 620 7 DG A 14 O6 96.8 72.9 116.7 167.2 118.0 72.4 REMARK 620 8 DG A 15 O6 72.0 119.7 166.6 111.3 71.9 97.7 67.6 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 PB B 101 PB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 1 O6 REMARK 620 2 DG B 2 O6 69.2 REMARK 620 3 DG B 5 O6 118.4 72.6 REMARK 620 4 DG B 6 O6 71.3 98.2 68.5 REMARK 620 5 DG B 10 O6 112.4 167.2 96.3 71.2 REMARK 620 6 DG B 11 O6 168.4 112.4 72.2 118.9 68.7 REMARK 620 7 DG B 14 O6 96.2 73.1 116.4 166.9 118.6 73.9 REMARK 620 8 DG B 15 O6 72.0 119.6 167.2 111.0 71.9 98.1 67.2 REMARK 620 N 1 2 3 4 5 6 7 DBREF 7D31 A 1 15 PDB 7D31 7D31 1 15 DBREF 7D31 B 1 15 PDB 7D31 7D31 1 15 SEQRES 1 A 15 DG DG DT DT DG DG DT DG DT DG DG DT DT SEQRES 2 A 15 DG DG SEQRES 1 B 15 DG DG DT DT DG DG DT DG DT DG DG DT DT SEQRES 2 B 15 DG DG HET PB A 101 1 HET PB B 101 1 HETNAM PB LEAD (II) ION FORMUL 3 PB 2(PB 2+) FORMUL 5 HOH *57(H2 O) LINK O6 DG A 1 PB PB A 101 1555 1555 2.60 LINK O6 DG A 2 PB PB A 101 1555 1555 2.65 LINK O6 DG A 5 PB PB A 101 1555 1555 2.59 LINK O6 DG A 6 PB PB A 101 1555 1555 2.75 LINK O6 DG A 10 PB PB A 101 1555 1555 2.59 LINK O6 DG A 11 PB PB A 101 1555 1555 2.66 LINK O6 DG A 14 PB PB A 101 1555 1555 2.61 LINK O6 DG A 15 PB PB A 101 1555 1555 2.72 LINK O6 DG B 1 PB PB B 101 1555 1555 2.56 LINK O6 DG B 2 PB PB B 101 1555 1555 2.70 LINK O6 DG B 5 PB PB B 101 1555 1555 2.60 LINK O6 DG B 6 PB PB B 101 1555 1555 2.76 LINK O6 DG B 10 PB PB B 101 1555 1555 2.65 LINK O6 DG B 11 PB PB B 101 1555 1555 2.60 LINK O6 DG B 14 PB PB B 101 1555 1555 2.59 LINK O6 DG B 15 PB PB B 101 1555 1555 2.73 CRYST1 40.017 40.017 99.896 90.00 90.00 90.00 P 41 21 2 16 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 0.024989 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024989 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010010 0.00000