HEADER DNA BINDING PROTEIN 09-NOV-17 6EXU TITLE CRYSTAL STRUCTURE OF THE DNA BINDING DOMAIN OF FISSION YEAST SAP1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SWITCH-ACTIVATING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 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: SAP1, SPCC1672.02C; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS S. POMBE, MATING TYPE SWITCH, DNA REPLICATION, MYB DOMAIN, DNA KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.EKUNDAYO,M.JOERGENSEN,T.SCHALCH REVDAT 1 28-NOV-18 6EXU 0 JRNL AUTH M.M.JORGENSEN,B.EKUNDAYO,M.ZARATIEGUI,K.SKRIVER,G.THON, JRNL AUTH 2 T.SCHALCH JRNL TITL STRUCTURE OF THE REPLICATION REGULATOR SAP1 REVEALS JRNL TITL 2 FUNCTIONALLY IMPORTANT INTERFACES. JRNL REF SCI REP V. 8 10930 2018 JRNL REFN ESSN 2045-2322 JRNL PMID 30026545 JRNL DOI 10.1038/S41598-018-29198-9 REMARK 2 REMARK 2 RESOLUTION. 1.41 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) : 1.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 20477 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1028 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 35.4012 - 2.6950 1.00 2951 157 0.1646 0.1825 REMARK 3 2 2.6950 - 2.1391 1.00 2833 129 0.1589 0.1827 REMARK 3 3 2.1391 - 1.8688 1.00 2775 140 0.1659 0.2154 REMARK 3 4 1.8688 - 1.6979 1.00 2751 158 0.1748 0.2095 REMARK 3 5 1.6979 - 1.5762 1.00 2765 141 0.1727 0.2280 REMARK 3 6 1.5762 - 1.4833 1.00 2720 161 0.1845 0.1971 REMARK 3 7 1.4833 - 1.4090 0.97 2654 142 0.2204 0.2577 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.290 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.008 895 REMARK 3 ANGLE : 0.973 1201 REMARK 3 CHIRALITY : 0.063 129 REMARK 3 PLANARITY : 0.006 155 REMARK 3 DIHEDRAL : 19.630 356 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 6EXU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1200007427. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-AUG-14 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 : SLS REMARK 200 BEAMLINE : X06DA 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 PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20477 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 35.390 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.02145 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.7600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.41 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.18860 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.620 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SPG BUFFER (SUCCINIC ACID, REMARK 280 PHOSPHATE, GLYCINE) PH 7.0, 25% PEG 1500, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 17.79100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.39000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.41550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.39000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.79100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.41550 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 LEU A 18 REMARK 465 SER A 19 REMARK 465 PRO A 20 REMARK 465 SER A 21 REMARK 465 SER A 22 REMARK 465 SER A 23 REMARK 465 PRO A 24 REMARK 465 ALA A 25 REMARK 465 LYS A 26 REMARK 465 ALA A 27 REMARK 465 GLN A 28 REMARK 465 ARG A 29 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6EXT RELATED DB: PDB DBREF 6EXU A 18 133 UNP P40847 SAP1_SCHPO 18 133 SEQRES 1 A 116 LEU SER PRO SER SER SER PRO ALA LYS ALA GLN ARG THR SEQRES 2 A 116 HIS LEU SER LEU GLU GLU LYS ILE LYS LEU MSE ARG LEU SEQRES 3 A 116 VAL VAL ARG HIS LYS HIS GLU LEU VAL ASP ARG LYS THR SEQRES 4 A 116 SER GLU PHE TYR ALA LYS ILE ALA ARG ILE GLY TYR GLU SEQRES 5 A 116 ASP GLU GLY LEU ALA ILE HIS THR GLU SER ALA CAS ARG SEQRES 6 A 116 ASN GLN ILE ILE SER ILE MSE ARG VAL TYR GLU GLN ARG SEQRES 7 A 116 LEU ALA HIS ARG GLN PRO GLY MSE LYS THR THR PRO GLU SEQRES 8 A 116 GLU ASP GLU LEU ASP GLN LEU CYS ASP GLU TRP LYS ALA SEQRES 9 A 116 ARG LEU SER GLU LEU GLN GLN TYR ARG GLU LYS PHE MODRES 6EXU MSE A 41 MET MODIFIED RESIDUE MODRES 6EXU CAS A 81 CYS MODIFIED RESIDUE MODRES 6EXU MSE A 89 MET MODIFIED RESIDUE MODRES 6EXU MSE A 103 MET MODIFIED RESIDUE HET MSE A 41 17 HET CAS A 81 9 HET MSE A 89 17 HET MSE A 103 17 HETNAM MSE SELENOMETHIONINE HETNAM CAS S-(DIMETHYLARSENIC)CYSTEINE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 1 CAS C5 H12 AS N O2 S FORMUL 2 HOH *125(H2 O) HELIX 1 AA1 SER A 33 HIS A 47 1 15 HELIX 2 AA2 LYS A 48 LEU A 51 5 4 HELIX 3 AA3 LYS A 55 GLY A 72 1 18 HELIX 4 AA4 THR A 77 ARG A 99 1 23 HELIX 5 AA5 THR A 106 PHE A 133 1 28 LINK C LEU A 40 N MSE A 41 1555 1555 1.33 LINK C MSE A 41 N ARG A 42 1555 1555 1.34 LINK C ALA A 80 N CAS A 81 1555 1555 1.32 LINK C CAS A 81 N ARG A 82 1555 1555 1.32 LINK C ILE A 88 N MSE A 89 1555 1555 1.32 LINK C MSE A 89 N ARG A 90 1555 1555 1.33 LINK C GLY A 102 N MSE A 103 1555 1555 1.33 LINK C MSE A 103 N LYS A 104 1555 1555 1.33 CRYST1 35.582 40.831 70.780 90.00 90.00 90.00 P 21 21 21 4 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 0.028104 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024491 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014128 0.00000