HEADER DNA 27-SEP-22 8GZK TITLE CRYSTAL STRUCTURE OF CD2+-BOUND DNA APTAMER T10A MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: 25-MER DNA; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS DNA APTAMER, CD2+-BINDING, COMPLEX, DNA EXPDTA X-RAY DIFFRACTION AUTHOR J.H.GAN,H.H.LIU,Y.Q.GAO REVDAT 2 29-MAY-24 8GZK 1 REMARK REVDAT 1 09-AUG-23 8GZK 0 JRNL AUTH H.LIU,Y.GAO,J.MATHIVANAN,Z.ARMOUR-GARB,Z.SHAO,Y.ZHANG, JRNL AUTH 2 X.ZHAO,Q.SHAO,W.ZHANG,J.YANG,C.CAO,H.LI,J.SHENG,J.GAN JRNL TITL CRYSTAL STRUCTURES AND IDENTIFICATION OF NOVEL CD2+-SPECIFIC JRNL TITL 2 DNA APTAMER. JRNL REF NUCLEIC ACIDS RES. V. 51 4625 2023 JRNL REFN ESSN 1362-4962 JRNL PMID 37013991 JRNL DOI 10.1093/NAR/GKAD239 REMARK 2 REMARK 2 RESOLUTION. 2.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 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) : 2.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.470 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.6 REMARK 3 NUMBER OF REFLECTIONS : 3634 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.450 REMARK 3 FREE R VALUE TEST SET COUNT : 307 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 28.0800 - 3.7100 0.99 1864 148 0.2166 0.2772 REMARK 3 2 3.7100 - 2.9400 0.80 1463 159 0.2544 0.3076 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.810 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.38 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.32 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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): 0.6685 27.7067 12.8518 REMARK 3 T TENSOR REMARK 3 T11: 0.3032 T22: 0.0528 REMARK 3 T33: 0.3590 T12: -1.3108 REMARK 3 T13: -0.3752 T23: -0.0884 REMARK 3 L TENSOR REMARK 3 L11: 0.5951 L22: 0.4213 REMARK 3 L33: -0.0697 L12: 0.6489 REMARK 3 L13: 0.2018 L23: 0.1508 REMARK 3 S TENSOR REMARK 3 S11: -0.2120 S12: 0.1464 S13: 0.4555 REMARK 3 S21: -0.1393 S22: -0.0139 S23: 0.0113 REMARK 3 S31: -0.6825 S32: 0.4039 S33: -0.0099 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 AND (RESID 1 THROUGH 9 OR RESID REMARK 3 11 THROUGH 25)) REMARK 3 SELECTION : (CHAIN B AND (RESID 1 THROUGH 9 OR RESID REMARK 3 11 THROUGH 25)) REMARK 3 ATOM PAIRS NUMBER : 466 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8GZK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 05-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1300032514. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-20 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) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3980 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.940 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 (%) : 97.4 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.41500 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: 8GZJ REMARK 200 REMARK 200 REMARK: ROD REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% MPD, PH 7.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 14.35400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 68.18950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 14.35400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 68.18950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DG A 7 O3' DG A 7 C3' -0.069 REMARK 500 DG A 8 O3' DG A 8 C3' -0.043 REMARK 500 DG A 9 O3' DG A 9 C3' -0.061 REMARK 500 DC A 12 O3' DC A 12 C3' -0.068 REMARK 500 DT A 17 O3' DT A 17 C3' -0.061 REMARK 500 DC A 18 O3' DC A 18 C3' -0.067 REMARK 500 DC A 19 O3' DG A 20 P -0.088 REMARK 500 DC B 3 O3' DC B 3 C3' -0.045 REMARK 500 DG B 8 O3' DG B 9 P -0.100 REMARK 500 DG B 9 O3' DG B 9 C3' -0.038 REMARK 500 DC B 19 O3' DC B 19 C3' -0.072 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 8 O5' - P - OP1 ANGL. DEV. = -6.4 DEGREES REMARK 500 DA A 15 O5' - P - OP1 ANGL. DEV. = -5.7 DEGREES REMARK 500 DA A 15 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC A 25 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA B 2 O5' - P - OP1 ANGL. DEV. = -6.7 DEGREES REMARK 500 DC B 14 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DA B 15 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG B 23 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT B 24 O4' - C1' - N1 ANGL. DEV. = 2.3 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 CD A 101 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 9 N7 REMARK 620 2 DC A 12 O2 112.9 REMARK 620 3 DC A 12 N3 93.7 53.8 REMARK 620 4 DG A 16 N7 84.3 162.1 122.8 REMARK 620 5 HOH A 201 O 157.0 61.9 64.7 100.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD B 101 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 9 N7 REMARK 620 2 DC B 12 O2 105.5 REMARK 620 3 DC B 12 N3 88.4 52.0 REMARK 620 4 DG B 16 N7 97.5 156.0 137.1 REMARK 620 5 HOH B 201 O 106.6 53.3 105.2 113.5 REMARK 620 N 1 2 3 4 DBREF 8GZK A 1 25 PDB 8GZK 8GZK 1 25 DBREF 8GZK B 1 25 PDB 8GZK 8GZK 1 25 SEQRES 1 A 25 DG DA DC DG DA DC DG DG DG DA DT DC DA SEQRES 2 A 25 DC DA DG DT DC DC DG DT DT DG DT DC SEQRES 1 B 25 DG DA DC DG DA DC DG DG DG DA DT DC DA SEQRES 2 B 25 DC DA DG DT DC DC DG DT DT DG DT DC HET CD A 101 1 HET BA A 102 1 HET BA A 103 1 HET BA A 104 1 HET CD B 101 1 HET BA B 102 1 HET BA B 103 1 HETNAM CD CADMIUM ION HETNAM BA BARIUM ION FORMUL 3 CD 2(CD 2+) FORMUL 4 BA 5(BA 2+) FORMUL 10 HOH *2(H2 O) LINK O6 DG A 1 BA BA A 103 1555 1555 3.42 LINK N7 DG A 9 CD CD A 101 1555 1555 2.34 LINK O2 DC A 12 CD CD A 101 1555 1555 2.59 LINK N3 DC A 12 CD CD A 101 1555 1555 2.51 LINK N7 DG A 16 CD CD A 101 1555 1555 2.51 LINK CD CD A 101 O HOH A 201 1555 1555 2.44 LINK N7 DG B 9 CD CD B 101 1555 1555 2.61 LINK O2 DC B 12 CD CD B 101 1555 1555 2.65 LINK N3 DC B 12 CD CD B 101 1555 1555 2.51 LINK N7 DG B 16 CD CD B 101 1555 1555 2.46 LINK CD CD B 101 O HOH B 201 1555 1555 2.60 CRYST1 28.708 136.379 51.133 90.00 104.39 90.00 C 1 2 1 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 0.034833 0.000000 0.008936 0.00000 SCALE2 0.000000 0.007333 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020190 0.00000