HEADER DNA BINDING PROTEIN 17-APR-16 5JDK TITLE CRYSTAL STRUCTURE OF THE DNA BINDING DOMAIN OF SAP1 IN FISSION YEAST TITLE 2 S.POMBE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SWITCH-ACTIVATING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-135; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE; SOURCE 3 ORGANISM_COMMON: FISSION YEAST; SOURCE 4 ORGANISM_TAXID: 284812; SOURCE 5 STRAIN: 972 / ATCC 24843; SOURCE 6 GENE: SAP1, SPCC1672.02C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS DNA REPLICATION, ALPHA-HELIX, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.HE,T.WANG REVDAT 4 20-MAR-24 5JDK 1 REMARK REVDAT 3 24-JAN-18 5JDK 1 JRNL REVDAT 2 18-OCT-17 5JDK 1 REMARK REVDAT 1 22-FEB-17 5JDK 0 JRNL AUTH L.GUAN,P.HE,F.YANG,Y.ZHANG,Y.HU,J.DING,Y.HUA,Y.ZHANG,Q.YE, JRNL AUTH 2 J.HU,T.WANG,C.JIN,D.KONG JRNL TITL SAP1 IS A REPLICATION-INITIATION FACTOR ESSENTIAL FOR THE JRNL TITL 2 ASSEMBLY OF PRE-REPLICATIVE COMPLEX IN THE FISSION YEAST JRNL TITL 3 SCHIZOSACCHAROMYCES POMBE. JRNL REF J. BIOL. CHEM. V. 292 6056 2017 JRNL REFN ESSN 1083-351X JRNL PMID 28223353 JRNL DOI 10.1074/JBC.M116.767806 REMARK 2 REMARK 2 RESOLUTION. 1.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 58139 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) : 0.170 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.430 REMARK 3 FREE R VALUE TEST SET COUNT : 1997 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 18.4231 - 2.4037 1.00 4251 151 0.1582 0.1610 REMARK 3 2 2.4037 - 1.9085 1.00 4113 146 0.1538 0.1525 REMARK 3 3 1.9085 - 1.6674 1.00 4056 145 0.1601 0.1683 REMARK 3 4 1.6674 - 1.5151 1.00 4027 144 0.1501 0.1694 REMARK 3 5 1.5151 - 1.4065 1.00 4002 142 0.1583 0.1803 REMARK 3 6 1.4065 - 1.3236 1.00 4007 142 0.1675 0.1799 REMARK 3 7 1.3236 - 1.2573 1.00 3998 143 0.1746 0.2110 REMARK 3 8 1.2573 - 1.2026 1.00 3970 142 0.1843 0.2071 REMARK 3 9 1.2026 - 1.1563 1.00 3995 142 0.1802 0.1908 REMARK 3 10 1.1563 - 1.1164 1.00 3948 141 0.1864 0.1938 REMARK 3 11 1.1164 - 1.0815 1.00 3977 140 0.2122 0.2242 REMARK 3 12 1.0815 - 1.0506 1.00 3973 141 0.2472 0.2663 REMARK 3 13 1.0506 - 1.0230 1.00 3941 140 0.2667 0.2849 REMARK 3 14 1.0230 - 0.9980 0.98 3884 138 0.2967 0.2881 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.910 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 : 0.006 897 REMARK 3 ANGLE : 0.911 1203 REMARK 3 CHIRALITY : 0.068 131 REMARK 3 PLANARITY : 0.006 154 REMARK 3 DIHEDRAL : 16.824 360 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' REMARK 3 ORIGIN FOR THE GROUP (A): -21.3255 1.9302 79.2675 REMARK 3 T TENSOR REMARK 3 T11: 0.0473 T22: 0.0473 REMARK 3 T33: 0.0437 T12: 0.0005 REMARK 3 T13: 0.0020 T23: -0.0004 REMARK 3 L TENSOR REMARK 3 L11: 0.2468 L22: 0.5216 REMARK 3 L33: 0.4605 L12: 0.1037 REMARK 3 L13: 0.1617 L23: -0.0014 REMARK 3 S TENSOR REMARK 3 S11: 0.0069 S12: 0.0253 S13: 0.0536 REMARK 3 S21: -0.0109 S22: -0.0135 S23: 0.0173 REMARK 3 S31: 0.0052 S32: -0.0067 S33: 0.0074 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 5JDK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000220407. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-NOV-13; 15-SEP-13 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 8.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; N REMARK 200 RADIATION SOURCE : SSRF; SEALED TUBE REMARK 200 BEAMLINE : BL17U; NULL REMARK 200 X-RAY GENERATOR MODEL : NULL; RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915; 1.5418 REMARK 200 MONOCHROMATOR : SI111; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R; RIGAKU SATURN REMARK 200 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 0.98.691 REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR 1.44 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58240 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.998 REMARK 200 RESOLUTION RANGE LOW (A) : 17.870 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.200 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.8800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.59800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.220 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX 1.10.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: HEXAGONAL PRISM, ROD REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 24.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200MM TRIMETHYLAMINE N-OXIDE, 15-22% REMARK 280 (W/V) PEG 2000MME, PH 8.8, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 18.42000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.07000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.44000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.07000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.42000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.44000 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 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 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 ALA A 3 REMARK 465 PRO A 4 REMARK 465 LYS A 5 REMARK 465 MET A 6 REMARK 465 GLU A 7 REMARK 465 LEU A 8 REMARK 465 LYS A 9 REMARK 465 SER A 10 REMARK 465 TYR A 11 REMARK 465 LYS A 12 REMARK 465 ARG A 13 REMARK 465 LYS A 14 REMARK 465 ASN A 15 REMARK 465 ALA A 16 REMARK 465 SER A 17 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 465 THR A 30 REMARK 465 HIS A 31 REMARK 465 PRO A 136 REMARK 465 ARG A 137 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 310 O HOH A 455 1.95 REMARK 500 O HOH A 464 O HOH A 490 2.08 REMARK 500 O HOH A 410 O HOH A 452 2.10 REMARK 500 ND2 ASN A 83 O HOH A 301 2.13 REMARK 500 O HOH A 381 O HOH A 464 2.14 REMARK 500 O HOH A 309 O HOH A 388 2.14 REMARK 500 O HOH A 301 O HOH A 404 2.15 REMARK 500 O HOH A 389 O HOH A 483 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 312 O HOH A 330 4547 2.05 REMARK 500 O HOH A 380 O HOH A 458 1655 2.08 REMARK 500 O HOH A 330 O HOH A 445 4447 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 201 DBREF 5JDK A 1 135 UNP P40847 SAP1_SCHPO 1 135 SEQADV 5JDK PRO A 136 UNP P40847 EXPRESSION TAG SEQADV 5JDK ARG A 137 UNP P40847 EXPRESSION TAG SEQRES 1 A 137 MET GLU ALA PRO LYS MET GLU LEU LYS SER TYR LYS ARG SEQRES 2 A 137 LYS ASN ALA SER LEU SER PRO SER SER SER PRO ALA LYS SEQRES 3 A 137 ALA GLN ARG THR HIS LEU SER LEU GLU GLU LYS ILE LYS SEQRES 4 A 137 LEU MET ARG LEU VAL VAL ARG HIS LYS HIS GLU LEU VAL SEQRES 5 A 137 ASP ARG LYS THR SER GLU PHE TYR ALA LYS ILE ALA ARG SEQRES 6 A 137 ILE GLY TYR GLU ASP GLU GLY LEU ALA ILE HIS THR GLU SEQRES 7 A 137 SER ALA CYS ARG ASN GLN ILE ILE SER ILE MET ARG VAL SEQRES 8 A 137 TYR GLU GLN ARG LEU ALA HIS ARG GLN PRO GLY MET LYS SEQRES 9 A 137 THR THR PRO GLU GLU ASP GLU LEU ASP GLN LEU CYS ASP SEQRES 10 A 137 GLU TRP LYS ALA ARG LEU SER GLU LEU GLN GLN TYR ARG SEQRES 11 A 137 GLU LYS PHE LEU VAL PRO ARG HET GOL A 201 14 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *200(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 LYS A 132 1 27 SITE 1 AC1 9 TYR A 60 ARG A 65 GLU A 69 ARG A 82 SITE 2 AC1 9 ILE A 85 ILE A 86 TRP A 119 HOH A 333 SITE 3 AC1 9 HOH A 394 CRYST1 36.840 40.880 70.140 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 0.027144 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024462 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014257 0.00000