PDB Short entry for 1GVJ HEADER TRANSCRIPTION 14-FEB-02 1GVJ TITLE ETS-1 DNA BINDING AND AUTOINHIBITORY DOMAINS COMPND MOL_ID: 1; COMPND 2 MOLECULE: C-ETS-1 PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 297-441; COMPND 5 SYNONYM: P54; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PAR2156 KEYWDS TRANSCRIPTION, ETS-1, AUTOINHIBITION, ETS DOMAIN EXPDTA X-RAY DIFFRACTION AUTHOR T.H.TAHIROV,K.OGATA REVDAT 4 13-DEC-23 1GVJ 1 REMARK REVDAT 3 08-MAY-19 1GVJ 1 REMARK REVDAT 2 24-FEB-09 1GVJ 1 VERSN REVDAT 1 06-FEB-04 1GVJ 0 JRNL AUTH T.H.TAHIROV,T.INOUE-BUNGO,K.OGATA JRNL TITL CRYSTAL STRUCTURE OF C-ETS-1 DNA-BINDING AND AUTOINHIBITORY JRNL TITL 2 DOMAINS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1125447.620 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.2 REMARK 3 NUMBER OF REFLECTIONS : 40277 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2010 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.53 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.63 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5884 REMARK 3 BIN R VALUE (WORKING SET) : 0.3280 REMARK 3 BIN FREE R VALUE : 0.3190 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 318 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2361 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 293 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.17000 REMARK 3 B22 (A**2) : -0.94000 REMARK 3 B33 (A**2) : -0.24000 REMARK 3 B12 (A**2) : -2.39000 REMARK 3 B13 (A**2) : 1.35000 REMARK 3 B23 (A**2) : -0.70000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.26 REMARK 3 LOW RESOLUTION CUTOFF (A) : 20.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.22 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.720 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.790 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.750 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.750 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.010 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 46.09 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1GVJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-FEB-02. REMARK 100 THE DEPOSITION ID IS D_1290009446. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUN-01 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL45XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.02 REMARK 200 MONOCHROMATOR : DIAMOND REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU IMAGE PLATE RAXIS V REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40937 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.520 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : 3.103 REMARK 200 R MERGE (I) : 0.10300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.6480 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.48400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.021 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1AWC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE, 30% W/V PEG REMARK 280 4000, 0.1 M SODIUM CITRATE PH 5.6, PROTEIN CONCENTRATION 15 MG/ REMARK 280 ML PLUS 10 MM DTT, TEMPERATURE 297 K, FOR CRYOPROTECTION 10% OF REMARK 280 PEG 400 WAS ADDED., PH 5.60 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 ASP A 438 REMARK 465 ALA A 439 REMARK 465 ASP A 440 REMARK 465 GLU A 441 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 PRO A 437 CA C O CB CG CD 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 ALA B 439 -72.28 -63.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B2152 DISTANCE = 5.92 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2STT RELATED DB: PDB REMARK 900 SOLUTION NMR STRUCTURE OF THE HUMAN ETS1/ DEOXYRIBONUCLEIC ACID REMARK 900 COMPLEX, 25 STRUCTURES REMARK 900 RELATED ID: 2STW RELATED DB: PDB REMARK 900 SOLUTION NMR STRUCTURE OF THE HUMAN ETS1/ DEOXYRIBONUCLEIC ACID REMARK 900 COMPLEX, RESTRAINED REGULARIZED MEAN STRUCTURE DBREF 1GVJ A 296 296 PDB 1GVJ 1GVJ 296 296 DBREF 1GVJ A 297 441 UNP P14921 ETS1_HUMAN 297 441 DBREF 1GVJ B 296 296 PDB 1GVJ 1GVJ 296 296 DBREF 1GVJ B 297 441 UNP P14921 ETS1_HUMAN 297 441 SEQRES 1 A 146 MET ASN HIS LYS PRO LYS GLY THR PHE LYS ASP TYR VAL SEQRES 2 A 146 ARG ASP ARG ALA ASP LEU ASN LYS ASP LYS PRO VAL ILE SEQRES 3 A 146 PRO ALA ALA ALA LEU ALA GLY TYR THR GLY SER GLY PRO SEQRES 4 A 146 ILE GLN LEU TRP GLN PHE LEU LEU GLU LEU LEU THR ASP SEQRES 5 A 146 LYS SER CYS GLN SER PHE ILE SER TRP THR GLY ASP GLY SEQRES 6 A 146 TRP GLU PHE LYS LEU SER ASP PRO ASP GLU VAL ALA ARG SEQRES 7 A 146 ARG TRP GLY LYS ARG LYS ASN LYS PRO LYS MET ASN TYR SEQRES 8 A 146 GLU LYS LEU SER ARG GLY LEU ARG TYR TYR TYR ASP LYS SEQRES 9 A 146 ASN ILE ILE HIS LYS THR ALA GLY LYS ARG TYR VAL TYR SEQRES 10 A 146 ARG PHE VAL CYS ASP LEU GLN SER LEU LEU GLY TYR THR SEQRES 11 A 146 PRO GLU GLU LEU HIS ALA MET LEU ASP VAL LYS PRO ASP SEQRES 12 A 146 ALA ASP GLU SEQRES 1 B 146 MET ASN HIS LYS PRO LYS GLY THR PHE LYS ASP TYR VAL SEQRES 2 B 146 ARG ASP ARG ALA ASP LEU ASN LYS ASP LYS PRO VAL ILE SEQRES 3 B 146 PRO ALA ALA ALA LEU ALA GLY TYR THR GLY SER GLY PRO SEQRES 4 B 146 ILE GLN LEU TRP GLN PHE LEU LEU GLU LEU LEU THR ASP SEQRES 5 B 146 LYS SER CYS GLN SER PHE ILE SER TRP THR GLY ASP GLY SEQRES 6 B 146 TRP GLU PHE LYS LEU SER ASP PRO ASP GLU VAL ALA ARG SEQRES 7 B 146 ARG TRP GLY LYS ARG LYS ASN LYS PRO LYS MET ASN TYR SEQRES 8 B 146 GLU LYS LEU SER ARG GLY LEU ARG TYR TYR TYR ASP LYS SEQRES 9 B 146 ASN ILE ILE HIS LYS THR ALA GLY LYS ARG TYR VAL TYR SEQRES 10 B 146 ARG PHE VAL CYS ASP LEU GLN SER LEU LEU GLY TYR THR SEQRES 11 B 146 PRO GLU GLU LEU HIS ALA MET LEU ASP VAL LYS PRO ASP SEQRES 12 B 146 ALA ASP GLU FORMUL 3 HOH *293(H2 O) HELIX 1 1 THR A 303 LEU A 314 1 12 HELIX 2 2 PRO A 322 GLY A 331 1 10 HELIX 3 3 GLN A 336 THR A 346 1 11 HELIX 4 4 ASP A 347 GLN A 351 5 5 HELIX 5 5 ASP A 367 ASN A 380 1 14 HELIX 6 6 ASN A 385 TYR A 396 1 12 HELIX 7 7 ASP A 417 GLY A 423 1 7 HELIX 8 8 THR A 425 LEU A 433 1 9 HELIX 9 9 THR B 303 ASP B 313 1 11 HELIX 10 10 PRO B 322 GLY B 331 1 10 HELIX 11 11 GLN B 336 THR B 346 1 11 HELIX 12 12 ASP B 347 GLN B 351 5 5 HELIX 13 13 ASP B 367 ASN B 380 1 14 HELIX 14 14 ASN B 385 LYS B 399 1 15 HELIX 15 15 ASP B 417 GLY B 423 1 7 HELIX 16 16 THR B 425 LEU B 433 1 9 SHEET 1 AA 4 SER A 355 TRP A 356 0 SHEET 2 AA 4 GLU A 362 LYS A 364 -1 O LYS A 364 N SER A 355 SHEET 3 AA 4 VAL A 411 PHE A 414 -1 O TYR A 412 N PHE A 363 SHEET 4 AA 4 ILE A 402 LYS A 404 -1 O HIS A 403 N ARG A 413 SHEET 1 BA 4 ILE B 354 TRP B 356 0 SHEET 2 BA 4 GLU B 362 LEU B 365 -1 O LYS B 364 N SER B 355 SHEET 3 BA 4 VAL B 411 PHE B 414 -1 O TYR B 412 N PHE B 363 SHEET 4 BA 4 ILE B 402 LYS B 404 -1 O HIS B 403 N ARG B 413 CRYST1 40.475 42.842 49.771 115.25 97.30 102.40 P 1 2 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 0.024707 0.005432 0.006463 0.00000 SCALE2 0.000000 0.023899 0.012673 0.00000 SCALE3 0.000000 0.000000 0.022928 0.00000 MTRIX1 1 0.286870 -0.957350 -0.034340 22.02220 1 MTRIX2 1 -0.957160 -0.287920 0.030660 27.59034 1 MTRIX3 1 -0.039240 0.024080 -0.998940 49.12850 1