HEADER TRANSCRIPTION/DNA 27-SEP-22 8EM9 TITLE HUMAN PU.1 ETS-DOMAIN (165-270) BOUND TO D(AATAGGAGAAGTAGGG) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*AP*AP*TP*AP*GP*GP*AP*GP*AP*AP*GP*TP*AP*GP*GP*G)- COMPND 3 3'); COMPND 4 CHAIN: C; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*TP*CP*CP*CP*TP*AP*CP*TP*TP*CP*TP*CP*CP*TP*A)- COMPND 8 3'); COMPND 9 CHAIN: D; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: TRANSCRIPTION FACTOR PU.1; COMPND 13 CHAIN: F; COMPND 14 FRAGMENT: ETS-DOMAIN UNP RESIDUES 165-270; COMPND 15 SYNONYM: 31 KDA-TRANSFORMING PROTEIN; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: SPI1; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSCRIPTION FACTOR, PROTEIN-DNA COMPLEX, ETS FAMILY, ETS, PU.1, KEYWDS 2 TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.R.TERRELL,G.M.K.POON REVDAT 2 25-OCT-23 8EM9 1 REMARK REVDAT 1 05-JUL-23 8EM9 0 JRNL AUTH J.R.TERRELL,S.J.TAYLOR,A.L.SCHNEIDER,Y.LU,T.N.VERNON, JRNL AUTH 2 S.XHANI,R.H.GUMPPER,M.LUO,W.D.WILSON,U.STEIDL,G.M.K.POON JRNL TITL DNA SELECTION BY THE MASTER TRANSCRIPTION FACTOR PU.1. JRNL REF CELL REP V. 42 12671 2023 JRNL REFN ESSN 2211-1247 JRNL PMID 37352101 JRNL DOI 10.1016/J.CELREP.2023.112671 REMARK 2 REMARK 2 RESOLUTION. 2.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 9123 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) : 0.223 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.170 REMARK 3 FREE R VALUE TEST SET COUNT : 928 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 24.1700 - 4.4700 1.00 1179 123 0.1648 0.2201 REMARK 3 2 4.4600 - 3.5500 1.00 1167 131 0.1979 0.2663 REMARK 3 3 3.5500 - 3.1000 0.99 1161 128 0.2152 0.2238 REMARK 3 4 3.1000 - 2.8200 1.00 1170 142 0.3124 0.3506 REMARK 3 5 2.8200 - 2.6200 1.00 1182 136 0.3050 0.3373 REMARK 3 6 2.6200 - 2.4600 1.00 1167 134 0.3344 0.3602 REMARK 3 7 2.4600 - 2.3410 1.00 1169 134 0.3677 0.4198 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) : 0.399 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.185 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.57 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.18 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 1471 REMARK 3 ANGLE : 0.570 2107 REMARK 3 CHIRALITY : 0.036 226 REMARK 3 PLANARITY : 0.003 155 REMARK 3 DIHEDRAL : 23.766 596 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 5.2791 13.6573 -3.4142 REMARK 3 T TENSOR REMARK 3 T11: 0.2965 T22: 0.7080 REMARK 3 T33: 0.2882 T12: -0.0849 REMARK 3 T13: -0.0297 T23: -0.0191 REMARK 3 L TENSOR REMARK 3 L11: 5.5072 L22: 5.4880 REMARK 3 L33: 9.4043 L12: -0.4945 REMARK 3 L13: -3.6882 L23: -2.5859 REMARK 3 S TENSOR REMARK 3 S11: -0.0578 S12: -0.2475 S13: -0.5986 REMARK 3 S21: -0.3473 S22: -0.3289 S23: 0.1757 REMARK 3 S31: 0.4361 S32: 0.0366 S33: 0.2005 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 8EM9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1000268638. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUL-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.920119 REMARK 200 MONOCHROMATOR : HORIZONTAL DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR (DCM) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9146 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.341 REMARK 200 RESOLUTION RANGE LOW (A) : 24.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.09712 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.1500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.84330 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.440 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: 8E3K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM ACETATE, PH=4.6, 2% PEG REMARK 280 3350, PH 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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 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 60.66133 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 30.33067 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: 3120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, 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 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 F 165 REMARK 465 SER F 166 REMARK 465 LYS F 167 REMARK 465 LYS F 168 REMARK 465 ARG F 259 REMARK 465 GLY F 260 REMARK 465 GLY F 261 REMARK 465 LEU F 262 REMARK 465 ALA F 263 REMARK 465 GLU F 264 REMARK 465 ARG F 265 REMARK 465 ARG F 266 REMARK 465 HIS F 267 REMARK 465 PRO F 268 REMARK 465 PRO F 269 REMARK 465 HIS F 270 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 DT D 33 C4' O4' C3' O3' C2' C1' N1 REMARK 470 DT D 33 C2 O2 N3 C4 O4 C5 C7 REMARK 470 DT D 33 C6 REMARK 470 LYS F 169 CG CD CE NZ REMARK 470 LYS F 237 CG CD CE NZ REMARK 470 LYS F 245 CG CD CE NZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASP F 184 O CG REMARK 480 LYS F 204 CD CE REMARK 480 ARG F 220 CZ 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 H22 DG C 7 O2 DC D 29 1.54 REMARK 500 OP2 DC D 24 HH TYR F 235 1.59 REMARK 500 REMARK 500 REMARK: NULL 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 ASP F 184 -82.06 -57.16 REMARK 500 ASP F 193 97.97 -165.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8E3K RELATED DB: PDB REMARK 900 RELATED ID: 8E3R RELATED DB: PDB REMARK 900 RELATED ID: 8E4H RELATED DB: PDB REMARK 900 RELATED ID: 8E5Y RELATED DB: PDB REMARK 900 RELATED ID: 8EBH RELATED DB: PDB REMARK 900 RELATED ID: 8EE9 RELATED DB: PDB REMARK 900 RELATED ID: 8EJ6 RELATED DB: PDB REMARK 900 RELATED ID: 8EJ8 RELATED DB: PDB REMARK 900 RELATED ID: 8EK3 RELATED DB: PDB REMARK 900 RELATED ID: 8EKJ RELATED DB: PDB REMARK 900 RELATED ID: 8EKU RELATED DB: PDB REMARK 900 RELATED ID: 8EKV RELATED DB: PDB REMARK 900 RELATED ID: 8EK8 RELATED DB: PDB REMARK 900 RELATED ID: 8EKZ RELATED DB: PDB DBREF 8EM9 C 2 17 PDB 8EM9 8EM9 2 17 DBREF 8EM9 D 18 33 PDB 8EM9 8EM9 18 33 DBREF 8EM9 F 165 270 UNP P17947 SPI1_HUMAN 165 270 SEQRES 1 C 16 DA DA DT DA DG DG DA DG DA DA DG DT DA SEQRES 2 C 16 DG DG DG SEQRES 1 D 16 DT DC DC DC DT DA DC DT DT DC DT DC DC SEQRES 2 D 16 DT DA DT SEQRES 1 F 106 GLY SER LYS LYS LYS ILE ARG LEU TYR GLN PHE LEU LEU SEQRES 2 F 106 ASP LEU LEU ARG SER GLY ASP MET LYS ASP SER ILE TRP SEQRES 3 F 106 TRP VAL ASP LYS ASP LYS GLY THR PHE GLN PHE SER SER SEQRES 4 F 106 LYS HIS LYS GLU ALA LEU ALA HIS ARG TRP GLY ILE GLN SEQRES 5 F 106 LYS GLY ASN ARG LYS LYS MET THR TYR GLN LYS MET ALA SEQRES 6 F 106 ARG ALA LEU ARG ASN TYR GLY LYS THR GLY GLU VAL LYS SEQRES 7 F 106 LYS VAL LYS LYS LYS LEU THR TYR GLN PHE SER GLY GLU SEQRES 8 F 106 VAL LEU GLY ARG GLY GLY LEU ALA GLU ARG ARG HIS PRO SEQRES 9 F 106 PRO HIS FORMUL 4 HOH *24(H2 O) HELIX 1 AA1 ARG F 171 GLY F 183 1 13 HELIX 2 AA2 HIS F 205 GLY F 218 1 14 HELIX 3 AA3 THR F 224 GLY F 239 1 16 HELIX 4 AA4 SER F 253 GLY F 258 1 6 SHEET 1 AA1 4 ILE F 189 ASP F 193 0 SHEET 2 AA1 4 THR F 198 PHE F 201 -1 O THR F 198 N VAL F 192 SHEET 3 AA1 4 THR F 249 PHE F 252 -1 O TYR F 250 N PHE F 199 SHEET 4 AA1 4 VAL F 241 LYS F 243 -1 N LYS F 242 O GLN F 251 CRYST1 46.184 46.184 90.992 90.00 90.00 120.00 P 32 3 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 0.021653 0.012501 0.000000 0.00000 SCALE2 0.000000 0.025002 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010990 0.00000