HEADER DNA BINDING PROTEIN 04-MAY-15 4ZMK TITLE CRYSTAL STRUCTURE OF THE DIMERIZATION DOMAIN OF S. POMBE TAZ1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TELOMERE LENGTH REGULATOR TAZ1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DIMERIZATION DOMAIN (UNP RESIDUES 408-478); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE (STRAIN 972 / ATCC SOURCE 3 24843); SOURCE 4 ORGANISM_COMMON: FISSION YEAST; SOURCE 5 ORGANISM_TAXID: 284812; SOURCE 6 STRAIN: 972 / ATCC 24843; SOURCE 7 GENE: TAZ1, MYB, MYB1, SPAC16A10.07C; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS TELOMERE, DIMERIZATION DOMAIN, FISSION YEAST, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR W.DENG,J.WU,F.WANG,M.LEI REVDAT 2 20-MAR-24 4ZMK 1 REMARK REVDAT 1 23-SEP-15 4ZMK 0 JRNL AUTH W.DENG,J.WU,F.WANG,J.KANOH,P.M.DEHE,H.INOUE,J.CHEN,M.LEI JRNL TITL FISSION YEAST TELOMERE-BINDING PROTEIN TAZ1 IS A FUNCTIONAL JRNL TITL 2 BUT NOT A STRUCTURAL COUNTERPART OF HUMAN TRF1 AND TRF2. JRNL REF CELL RES. V. 25 881 2015 JRNL REFN ISSN 1001-0602 JRNL PMID 26088418 JRNL DOI 10.1038/CR.2015.76 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 12585 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.440 REMARK 3 FREE R VALUE TEST SET COUNT : 170 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 1.5500 - 1.5000 0.97 3657 170 0.1592 0.2010 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.77 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.85 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 : 0.006 592 REMARK 3 ANGLE : 0.796 812 REMARK 3 CHIRALITY : 0.030 103 REMARK 3 PLANARITY : 0.003 104 REMARK 3 DIHEDRAL : 13.114 240 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 408:478) REMARK 3 ORIGIN FOR THE GROUP (A): 14.7409 7.6458 4.5671 REMARK 3 T TENSOR REMARK 3 T11: 0.2252 T22: 0.1642 REMARK 3 T33: 0.0470 T12: 0.0212 REMARK 3 T13: 0.0490 T23: 0.0121 REMARK 3 L TENSOR REMARK 3 L11: 2.8956 L22: 2.4129 REMARK 3 L33: 2.9021 L12: -0.0121 REMARK 3 L13: -0.4807 L23: 0.1860 REMARK 3 S TENSOR REMARK 3 S11: -0.2001 S12: -0.1855 S13: -0.0918 REMARK 3 S21: 0.2849 S22: -0.2015 S23: -0.1098 REMARK 3 S31: 0.3062 S32: 0.0942 S33: -0.0024 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 501:560) REMARK 3 ORIGIN FOR THE GROUP (A): 16.3073 8.0490 6.4745 REMARK 3 T TENSOR REMARK 3 T11: 0.3083 T22: 0.2450 REMARK 3 T33: 0.2850 T12: 0.0161 REMARK 3 T13: 0.0684 T23: -0.0614 REMARK 3 L TENSOR REMARK 3 L11: 2.3420 L22: 0.7866 REMARK 3 L33: 2.6237 L12: 0.1300 REMARK 3 L13: 0.9133 L23: 0.0053 REMARK 3 S TENSOR REMARK 3 S11: -0.1302 S12: -0.2222 S13: -0.0794 REMARK 3 S21: 0.1459 S22: -0.0442 S23: -0.0193 REMARK 3 S31: 0.3230 S32: 0.0937 S33: 0.1649 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 4ZMK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-MAY-15. REMARK 100 THE DEPOSITION ID IS D_1000209540. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-SEP-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13259 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.27100 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: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM BICINE PH8.5, 2.3M AMMONIUM REMARK 280 SULFATE, 10MM DTT, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 39.34350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 22.53900 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 22.53900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 59.01525 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 22.53900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 22.53900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 19.67175 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 22.53900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 22.53900 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 59.01525 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 22.53900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 22.53900 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 19.67175 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 39.34350 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: 2350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL 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 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 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 O HOH A 541 O HOH A 545 1.99 REMARK 500 O HOH A 523 O HOH A 537 2.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ZMI RELATED DB: PDB DBREF 4ZMK A 408 478 UNP P79005 TAZ1_SCHPO 408 478 SEQRES 1 A 71 ASP THR PHE SER GLU ARG THR LEU GLY LEU ASN SER ILE SEQRES 2 A 71 ASP ASN THR GLU ILE SER GLU VAL VAL SER LEU GLY LEU SEQRES 3 A 71 VAL SER SER ALA LEU ASP LYS ILE THR GLY LEU LEU SER SEQRES 4 A 71 ALA ASP ASN LEU SER GLU THR VAL SER GLN ALA ARG ASP SEQRES 5 A 71 PHE SER HIS THR LEU SER LYS SER LEU LYS SER ARG ALA SEQRES 6 A 71 LYS SER LEU SER GLN LYS FORMUL 2 HOH *60(H2 O) HELIX 1 AA1 THR A 409 LEU A 415 1 7 HELIX 2 AA2 SER A 426 ASP A 448 1 23 HELIX 3 AA3 LEU A 450 LYS A 478 1 29 CRYST1 45.078 45.078 78.687 90.00 90.00 90.00 P 43 21 2 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 0.022184 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022184 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012709 0.00000