HEADER DNA BINDING PROTEIN/DNA 22-AUG-22 8GN4 TITLE THE CRYSTAL STRUCTURE OF ZBTB10 ZF1-2 R767Q IN COMPLEX WITH TELOMERIC TITLE 2 DNA TTAGGG COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZINC FINGER AND BTB DOMAIN-CONTAINING PROTEIN 10; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ZINC FINGER PROTEIN RIN ZF; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*TP*A)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*AP*TP*AP*TP*AP*AP*CP*CP*CP*TP*A)-3'); COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ZBTB10; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS TELOMERIC DNA BINDING, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR F.D.LI,S.M.WANG REVDAT 2 24-APR-24 8GN4 1 JRNL REVDAT 1 30-AUG-23 8GN4 0 JRNL AUTH S.WANG,Z.XU,M.LI,M.LV,S.SHEN,Y.SHI,F.LI JRNL TITL STRUCTURAL INSIGHTS INTO THE RECOGNITION OF TELOMERIC JRNL TITL 2 VARIANT REPEAT TTGGGG BY BROAD-COMPLEX, TRAMTRACK AND JRNL TITL 3 BRIC-A-BRAC - ZINC FINGER PROTEIN ZBTB10. JRNL REF J.BIOL.CHEM. V. 299 02918 2023 JRNL REFN ESSN 1083-351X JRNL PMID 36657642 JRNL DOI 10.1016/J.JBC.2023.102918 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.980 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.2 REMARK 3 NUMBER OF REFLECTIONS : 8940 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 438 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 30.1880 - 2.7402 0.94 3048 153 0.1827 0.2364 REMARK 3 2 2.7402 - 2.1752 0.95 3103 156 0.2377 0.2848 REMARK 3 3 2.1752 - 1.9003 0.73 2351 129 0.2664 0.2912 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.66 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 : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 720 THROUGH 772) REMARK 3 ORIGIN FOR THE GROUP (A): 7.4103 -6.8330 13.7955 REMARK 3 T TENSOR REMARK 3 T11: 0.0798 T22: 0.0535 REMARK 3 T33: 0.1477 T12: -0.0205 REMARK 3 T13: 0.0202 T23: 0.0280 REMARK 3 L TENSOR REMARK 3 L11: 2.2830 L22: 1.9377 REMARK 3 L33: 3.9053 L12: -1.1738 REMARK 3 L13: -0.9047 L23: 2.2134 REMARK 3 S TENSOR REMARK 3 S11: 0.1041 S12: 0.0919 S13: 0.0748 REMARK 3 S21: -0.0414 S22: -0.0018 S23: -0.1085 REMARK 3 S31: -0.0652 S32: -0.1371 S33: -0.0852 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 1 THROUGH 11) REMARK 3 ORIGIN FOR THE GROUP (A): -0.5633 -10.6844 10.7708 REMARK 3 T TENSOR REMARK 3 T11: 0.1822 T22: 0.2040 REMARK 3 T33: 0.2003 T12: 0.0257 REMARK 3 T13: 0.0870 T23: 0.0576 REMARK 3 L TENSOR REMARK 3 L11: 1.5339 L22: 0.9916 REMARK 3 L33: 3.9699 L12: -0.0308 REMARK 3 L13: 1.6679 L23: -0.9399 REMARK 3 S TENSOR REMARK 3 S11: 0.2323 S12: 0.1977 S13: 0.0023 REMARK 3 S21: 0.1445 S22: 0.1181 S23: 0.1351 REMARK 3 S31: -0.3579 S32: 0.0947 S33: 0.0091 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'C' AND RESID 1 THROUGH 11) REMARK 3 ORIGIN FOR THE GROUP (A): -0.5808 -9.2181 8.9011 REMARK 3 T TENSOR REMARK 3 T11: 0.1755 T22: 0.1918 REMARK 3 T33: 0.0780 T12: -0.0441 REMARK 3 T13: 0.0479 T23: 0.0031 REMARK 3 L TENSOR REMARK 3 L11: 1.9334 L22: 0.8948 REMARK 3 L33: 1.2434 L12: -0.0171 REMARK 3 L13: -0.4171 L23: 0.3260 REMARK 3 S TENSOR REMARK 3 S11: 0.2625 S12: -0.0076 S13: 0.1318 REMARK 3 S21: 0.0794 S22: 0.0202 S23: 0.0718 REMARK 3 S31: -0.2385 S32: 0.2559 S33: -0.0318 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 8GN4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1300031777. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUN-19 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 : SSRF REMARK 200 BEAMLINE : BL19U1 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9392 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.30000 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: 8GN3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CACODYLATE, PH 6.5, 27 % REMARK 280 V/V PEG 2000 MME, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 713 REMARK 465 GLU A 714 REMARK 465 SER A 715 REMARK 465 SER A 716 REMARK 465 LEU A 717 REMARK 465 ILE A 718 REMARK 465 MET A 719 REMARK 465 LYS A 773 REMARK 465 LYS A 774 REMARK 465 ASP A 775 REMARK 465 LYS A 776 REMARK 465 LYS A 777 REMARK 465 TYR A 778 REMARK 465 LYS A 779 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 B 4 O4' - C1' - N9 ANGL. DEV. = 2.2 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 ZN A 801 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 724 SG REMARK 620 2 CYS A 727 SG 124.0 REMARK 620 3 HIS A 740 NE2 101.6 103.1 REMARK 620 4 HIS A 744 NE2 102.6 117.6 105.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 802 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 752 SG REMARK 620 2 CYS A 755 SG 113.9 REMARK 620 3 HIS A 768 NE2 110.3 102.3 REMARK 620 4 HIS A 772 NE2 105.3 116.9 107.9 REMARK 620 N 1 2 3 DBREF 8GN4 A 713 779 UNP Q96DT7 ZBT10_HUMAN 713 779 DBREF 8GN4 B 1 11 PDB 8GN4 8GN4 1 11 DBREF 8GN4 C 1 11 PDB 8GN4 8GN4 1 11 SEQADV 8GN4 GLN A 767 UNP Q96DT7 ARG 767 ENGINEERED MUTATION SEQRES 1 A 67 GLY GLU SER SER LEU ILE MET ASN LYS LEU LYS CYS PRO SEQRES 2 A 67 HIS CYS SER TYR VAL ALA LYS TYR ARG ARG THR LEU LYS SEQRES 3 A 67 ARG HIS LEU LEU ILE HIS THR GLY VAL ARG SER PHE SER SEQRES 4 A 67 CYS ASP ILE CYS GLY LYS LEU PHE THR ARG ARG GLU HIS SEQRES 5 A 67 VAL LYS GLN HIS SER LEU VAL HIS LYS LYS ASP LYS LYS SEQRES 6 A 67 TYR LYS SEQRES 1 B 11 DT DT DA DG DG DG DT DT DA DT DA SEQRES 1 C 11 DA DT DA DT DA DA DC DC DC DT DA HET ZN A 801 1 HET ZN A 802 1 HETNAM ZN ZINC ION FORMUL 4 ZN 2(ZN 2+) FORMUL 6 HOH *100(H2 O) HELIX 1 AA1 TYR A 733 LEU A 741 1 9 HELIX 2 AA2 LEU A 741 GLY A 746 1 6 HELIX 3 AA3 ARG A 761 SER A 769 1 9 HELIX 4 AA4 LEU A 770 HIS A 772 5 3 SHEET 1 AA1 2 PHE A 750 SER A 751 0 SHEET 2 AA1 2 LEU A 758 PHE A 759 -1 O PHE A 759 N PHE A 750 LINK SG CYS A 724 ZN ZN A 801 1555 1555 2.25 LINK SG CYS A 727 ZN ZN A 801 1555 1555 2.21 LINK NE2 HIS A 740 ZN ZN A 801 1555 1555 2.07 LINK NE2 HIS A 744 ZN ZN A 801 1555 1555 2.01 LINK SG CYS A 752 ZN ZN A 802 1555 1555 2.26 LINK SG CYS A 755 ZN ZN A 802 1555 1555 2.31 LINK NE2 HIS A 768 ZN ZN A 802 1555 1555 2.12 LINK NE2 HIS A 772 ZN ZN A 802 1555 1555 2.19 CRYST1 30.866 32.665 36.105 105.99 90.46 105.21 P 1 1 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 0.032398 0.008810 0.002917 0.00000 SCALE2 0.000000 0.031726 0.009531 0.00000 SCALE3 0.000000 0.000000 0.028921 0.00000