HEADER STRUCTURAL PROTEIN 04-SEP-17 5YBC TITLE X-RAY STRUCTURE OF NATIVE ETS-DOMAIN DOMAIN OF ERGP55 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR ERG; COMPND 3 CHAIN: C, A; COMPND 4 FRAGMENT: ETS DOMAIN, UNP RESIDUES 317-408; COMPND 5 SYNONYM: TRANSFORMING PROTEIN ERG; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ERG; SOURCE 6 EXPRESSION_SYSTEM: ENTEROBACTERIA PHAGE L1; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 268588 KEYWDS ETS TRANSCRIPTION FACTOR, ERGP55, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.K.SAXENA,S.P.GANGWAR REVDAT 3 27-MAR-24 5YBC 1 REMARK REVDAT 2 17-OCT-18 5YBC 1 JRNL REVDAT 1 19-SEP-18 5YBC 0 JRNL AUTH R.SHARMA,S.P.GANGWAR,A.K.SAXENA JRNL TITL COMPARATIVE STRUCTURE ANALYSIS OF THE ETSI DOMAIN OF ERG3 JRNL TITL 2 AND ITS COMPLEX WITH THE E74 PROMOTER DNA SEQUENCE JRNL REF ACTA CRYSTALLOGR F STRUCT V. 74 656 2018 JRNL REF 2 BIOL COMMUN JRNL REFN ESSN 2053-230X JRNL PMID 30279318 JRNL DOI 10.1107/S2053230X1801110X REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 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) : 32.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 9874 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 506 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 32.2852 - 3.9665 0.99 2456 144 0.1806 0.1899 REMARK 3 2 3.9665 - 3.1492 0.99 2311 126 0.2430 0.3197 REMARK 3 3 3.1492 - 2.7513 1.00 2316 123 0.3184 0.4184 REMARK 3 4 2.7513 - 2.4999 1.00 2285 113 0.2961 0.3547 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) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.790 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 60.86 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.22 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 : 0.010 1577 REMARK 3 ANGLE : 1.368 2119 REMARK 3 CHIRALITY : 0.056 209 REMARK 3 PLANARITY : 0.007 270 REMARK 3 DIHEDRAL : 14.628 594 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): -5.1384 0.3988 -18.7748 REMARK 3 T TENSOR REMARK 3 T11: 0.4755 T22: 0.4936 REMARK 3 T33: 0.4693 T12: -0.0009 REMARK 3 T13: -0.0684 T23: -0.0288 REMARK 3 L TENSOR REMARK 3 L11: 0.6909 L22: 0.6486 REMARK 3 L33: 0.5186 L12: -0.4174 REMARK 3 L13: 0.3326 L23: 0.3295 REMARK 3 S TENSOR REMARK 3 S11: 0.0376 S12: -0.1543 S13: 0.0560 REMARK 3 S21: 0.1166 S22: 0.1141 S23: -0.0453 REMARK 3 S31: 0.3221 S32: -0.0048 S33: 0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A AND SEGID A REMARK 3 SELECTION : CHAIN C AND SEGID C REMARK 3 ATOM PAIRS NUMBER : 867 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5YBC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1300004983. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0-5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : GRAZING ANGLE 2.8 MRAD REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9971 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 27.50 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 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) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 25.70 REMARK 200 R MERGE FOR SHELL (I) : 0.98900 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: RECTANGULAR BYPYRAMID REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20%(W/V) PEG400, 130MM NACL, 60MM REMARK 280 MGCL2, 100MM SODIUM CITRATE PH 5.6, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 64.15250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 32.28250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 32.28250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.07625 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 32.28250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 32.28250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 96.22875 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 32.28250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.28250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 32.07625 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 32.28250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 32.28250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 96.22875 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 64.15250 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 APPLY THE FOLLOWING TO CHAINS: C, 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 PRO C 401 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 LEU A 399 38.13 -70.97 REMARK 500 GLN A 400 -46.27 -132.15 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 501 DBREF 5YBC C 310 401 UNP P11308 ERG_HUMAN 317 408 DBREF 5YBC A 310 401 UNP P11308 ERG_HUMAN 317 408 SEQRES 1 C 92 GLN ILE GLN LEU TRP GLN PHE LEU LEU GLU LEU LEU SER SEQRES 2 C 92 ASP SER SER ASN SER SER CYS ILE THR TRP GLU GLY THR SEQRES 3 C 92 ASN GLY GLU PHE LYS MET THR ASP PRO ASP GLU VAL ALA SEQRES 4 C 92 ARG ARG TRP GLY GLU ARG LYS SER LYS PRO ASN MET ASN SEQRES 5 C 92 TYR ASP LYS LEU SER ARG ALA LEU ARG TYR TYR TYR ASP SEQRES 6 C 92 LYS ASN ILE MET THR LYS VAL HIS GLY LYS ARG TYR ALA SEQRES 7 C 92 TYR LYS PHE ASP PHE HIS GLY ILE ALA GLN ALA LEU GLN SEQRES 8 C 92 PRO SEQRES 1 A 92 GLN ILE GLN LEU TRP GLN PHE LEU LEU GLU LEU LEU SER SEQRES 2 A 92 ASP SER SER ASN SER SER CYS ILE THR TRP GLU GLY THR SEQRES 3 A 92 ASN GLY GLU PHE LYS MET THR ASP PRO ASP GLU VAL ALA SEQRES 4 A 92 ARG ARG TRP GLY GLU ARG LYS SER LYS PRO ASN MET ASN SEQRES 5 A 92 TYR ASP LYS LEU SER ARG ALA LEU ARG TYR TYR TYR ASP SEQRES 6 A 92 LYS ASN ILE MET THR LYS VAL HIS GLY LYS ARG TYR ALA SEQRES 7 A 92 TYR LYS PHE ASP PHE HIS GLY ILE ALA GLN ALA LEU GLN SEQRES 8 A 92 PRO HET GOL A 501 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL C3 H8 O3 HELIX 1 AA1 GLN C 312 ASP C 323 1 12 HELIX 2 AA2 SER C 324 CYS C 329 5 6 HELIX 3 AA3 ASP C 343 LYS C 355 1 13 HELIX 4 AA4 ASN C 361 TYR C 371 1 11 HELIX 5 AA5 TYR C 372 LYS C 375 5 4 HELIX 6 AA6 ASP C 391 GLN C 400 1 10 HELIX 7 AA7 GLN A 312 ASP A 323 1 12 HELIX 8 AA8 SER A 324 SER A 328 5 5 HELIX 9 AA9 ASP A 343 LYS A 355 1 13 HELIX 10 AB1 ASN A 361 TYR A 372 1 12 HELIX 11 AB2 TYR A 373 LYS A 375 5 3 HELIX 12 AB3 ASP A 391 LEU A 399 1 9 SHEET 1 AA1 4 THR C 331 GLU C 333 0 SHEET 2 AA1 4 GLU C 338 LYS C 340 -1 O GLU C 338 N GLU C 333 SHEET 3 AA1 4 ALA C 387 PHE C 390 -1 O TYR C 388 N PHE C 339 SHEET 4 AA1 4 MET C 378 LYS C 380 -1 N THR C 379 O LYS C 389 SHEET 1 AA2 4 ILE A 330 GLU A 333 0 SHEET 2 AA2 4 GLU A 338 MET A 341 -1 O LYS A 340 N THR A 331 SHEET 3 AA2 4 ALA A 387 PHE A 390 -1 O TYR A 388 N PHE A 339 SHEET 4 AA2 4 MET A 378 LYS A 380 -1 N THR A 379 O LYS A 389 CISPEP 1 PRO C 358 ASN C 359 0 -1.51 SITE 1 AC1 3 ARG A 370 LYS A 380 ARG A 385 CRYST1 64.565 64.565 128.305 90.00 90.00 90.00 P 41 21 2 16 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 0.015488 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015488 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007794 0.00000