HEADER DNA BINDING PROTEIN 18-MAY-20 7C4Q TITLE CRYSTAL STRUCTURE OF DBD PLASMA TREATED ZEBRAFISH TRF2 MYB-DOMAIN TITLE 2 COMPLEXED WITH DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: TERFA PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ZEBRAFISH TELOMERIC REPEAT BINDING FACTOR2; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3'); COMPND 8 CHAIN: C; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'-D(*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*A)-3'); COMPND 12 CHAIN: D, F; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: TERFA PROTEIN; COMPND 16 CHAIN: B; COMPND 17 SYNONYM: ZEBRAFISH TELOMERIC REPEAT BINDING FACTOR2; COMPND 18 ENGINEERED: YES; COMPND 19 MOL_ID: 5; COMPND 20 MOLECULE: DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3'); COMPND 21 CHAIN: E; COMPND 22 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: TERFA; 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; SOURCE 16 MOL_ID: 4; SOURCE 17 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 18 ORGANISM_COMMON: ZEBRAFISH; SOURCE 19 ORGANISM_TAXID: 7955; SOURCE 20 GENE: TERFA; SOURCE 21 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 22 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 23 MOL_ID: 5; SOURCE 24 SYNTHETIC: YES; SOURCE 25 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 26 ORGANISM_TAXID: 9606 KEYWDS ZEBRAFISH TRF2, TELOMERIC DNA, COMPLEX., DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Z.JIN,J.H.PARK,J.H.YUN,S.Y.PARK,W.LEE REVDAT 2 29-NOV-23 7C4Q 1 REMARK REVDAT 1 26-MAY-21 7C4Q 0 JRNL AUTH Y.JIN,J.H.PARK,J.H.YUN,S.Y.PARK,W.LEE JRNL TITL CRYSTAL STRUCTURE OF DBD PLASMA TREATED ZEBRAFISH TRF2 JRNL TITL 2 MYB-DOMAIN COMPLEXED WITH DNA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 12151 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.910 REMARK 3 FREE R VALUE TEST SET COUNT : 1204 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 36.2930 - 5.1960 1.00 1343 150 0.1809 0.2135 REMARK 3 2 5.1960 - 4.1261 1.00 1274 139 0.1969 0.1977 REMARK 3 3 4.1261 - 3.6050 1.00 1254 136 0.2215 0.2161 REMARK 3 4 3.6050 - 3.2757 1.00 1217 136 0.2234 0.2537 REMARK 3 5 3.2757 - 3.0410 1.00 1241 140 0.2379 0.2766 REMARK 3 6 3.0410 - 2.8618 1.00 1228 132 0.2809 0.3080 REMARK 3 7 2.8618 - 2.7185 1.00 1231 133 0.2915 0.3549 REMARK 3 8 2.7185 - 2.6002 0.96 1171 129 0.3234 0.3418 REMARK 3 9 2.6002 - 2.5001 0.82 988 109 0.4135 0.4845 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.420 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.970 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 57.03 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.73 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 : 0.003 1985 REMARK 3 ANGLE : 0.484 2864 REMARK 3 CHIRALITY : 0.029 308 REMARK 3 PLANARITY : 0.002 199 REMARK 3 DIHEDRAL : 22.094 1000 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 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7C4Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1300015666. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-NOV-15 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12151 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 36.297 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.1100 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) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.78300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 1W0U REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20-25% (W/V) POLYETHYLENE GLYCOL 3000, REMARK 280 100 MM SODIUM ACETATE/ACETIC ACID, PH 4.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 95.80400 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 47.90200 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 47.90200 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 95.80400 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, E, F 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: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS A 573 78.66 58.32 REMARK 500 PRO B 553 71.03 -69.46 REMARK 500 REMARK 500 REMARK: NULL DBREF 7C4Q A 521 574 UNP Q4QRH9 Q4QRH9_DANRE 520 573 DBREF 7C4Q C 1 12 PDB 7C4Q 7C4Q 1 12 DBREF 7C4Q D 1 12 PDB 7C4Q 7C4Q 1 12 DBREF 7C4Q B 521 575 UNP Q4QRH9 Q4QRH9_DANRE 520 574 DBREF 7C4Q E 1 10 PDB 7C4Q 7C4Q 1 10 DBREF 7C4Q F 1 12 PDB 7C4Q 7C4Q 1 12 SEQRES 1 A 54 THR ARG LYS MET TRP SER VAL GLN GLU SER GLU TRP LEU SEQRES 2 A 54 LYS GLN GLY VAL VAL ARG TYR GLY VAL GLY HIS TRP GLU SEQRES 3 A 54 ARG ILE ARG SER ALA PHE PRO PHE ALA GLY ARG THR ALA SEQRES 4 A 54 VAL ASN LEU LYS ASP ARG TRP ARG THR MET VAL LYS LEU SEQRES 5 A 54 LYS MET SEQRES 1 C 12 DT DT DA DG DG DG DT DT DA DG DG DG SEQRES 1 D 12 DC DC DC DT DA DA DC DC DC DT DA DA SEQRES 1 B 55 THR ARG LYS MET TRP SER VAL GLN GLU SER GLU TRP LEU SEQRES 2 B 55 LYS GLN GLY VAL VAL ARG TYR GLY VAL GLY HIS TRP GLU SEQRES 3 B 55 ARG ILE ARG SER ALA PHE PRO PHE ALA GLY ARG THR ALA SEQRES 4 B 55 VAL ASN LEU LYS ASP ARG TRP ARG THR MET VAL LYS LEU SEQRES 5 B 55 LYS MET VAL SEQRES 1 E 10 DT DT DA DG DG DG DT DT DA DG SEQRES 1 F 12 DC DC DC DT DA DA DC DC DC DT DA DA FORMUL 7 HOH *13(H2 O) HELIX 1 AA1 SER A 526 GLY A 541 1 16 HELIX 2 AA2 HIS A 544 PHE A 552 1 9 HELIX 3 AA3 THR A 558 LEU A 572 1 15 HELIX 4 AA4 SER B 526 GLY B 541 1 16 HELIX 5 AA5 HIS B 544 PHE B 552 1 9 HELIX 6 AA6 THR B 558 LEU B 572 1 15 CRYST1 64.211 64.211 143.706 90.00 90.00 120.00 P 32 2 1 12 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 0.015574 0.008991 0.000000 0.00000 SCALE2 0.000000 0.017983 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006959 0.00000