HEADER TRANSCRIPTION 11-SEP-09 3JTG TITLE CRYSTAL STRUCTURE OF MOUSE ELF3 C-TERMINAL DNA-BINDING DOMAIN IN TITLE 2 COMPLEX WITH TYPE II TGF-BETA RECEPTOR PROMOTER DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ETS-RELATED TRANSCRIPTION FACTOR ELF-3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 289-391; COMPND 5 SYNONYM: E74-LIKE FACTOR 3, EPITHELIUM-SPECIFIC ETS TRANSCRIPTION COMPND 6 FACTOR 1, ESE-1, EPITHELIUM-RESTRICTED ETS PROTEIN ESX, EPITHELIAL- COMPND 7 RESTRICTED WITH SERINE BOX; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(*GP*AP*GP*GP*AP*GP*TP*TP*TP*CP*CP*TP*GP*TP*TP*T)- COMPND 11 3'); COMPND 12 CHAIN: B; COMPND 13 ENGINEERED: YES; COMPND 14 OTHER_DETAILS: TYPE II TGF-BETA RECEPTOR PROMOTER DNA; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: DNA (5'-D(*CP*AP*AP*AP*CP*AP*GP*GP*AP*AP*AP*CP*TP*CP*CP*T)- COMPND 17 3'); COMPND 18 CHAIN: C; COMPND 19 ENGINEERED: YES; COMPND 20 OTHER_DETAILS: TYPE II TGF-BETA RECEPTOR PROMOTER DNA SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: ELF3, ERT, ESX, JEN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) E.COLI; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-28B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: SEQUENCES OBTAINED FROM TYPE II TGF-BETA RECEPTOR SOURCE 14 PROMOTER DNA; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 OTHER_DETAILS: SEQUENCES OBTAINED FROM TYPE II TGF-BETA RECEPTOR SOURCE 18 PROMOTER DNA KEYWDS ELF3, PROTEIN-DNA COMPLEX, TYPE II TGF-BETA RECEPTOR, ACTIVATOR, KEYWDS 2 ALTERNATIVE SPLICING, CYTOPLASM, DEVELOPMENTAL PROTEIN, KEYWDS 3 DIFFERENTIATION, DNA-BINDING, INFLAMMATORY RESPONSE, NUCLEUS, KEYWDS 4 REPRESSOR, TRANSCRIPTION, TRANSCRIPTION REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR T.H.TAHIROV,N.D.BABAYEVA,V.B.AGARKAR,A.RIZZINO REVDAT 3 21-FEB-24 3JTG 1 DBREF REVDAT 2 28-APR-10 3JTG 1 JRNL REVDAT 1 12-JAN-10 3JTG 0 JRNL AUTH V.B.AGARKAR,N.D.BABAYEVA,P.J.WILDER,A.RIZZINO,T.H.TAHIROV JRNL TITL CRYSTAL STRUCTURE OF MOUSE ELF3 C-TERMINAL DNA-BINDING JRNL TITL 2 DOMAIN IN COMPLEX WITH TYPE II TGF-BETA RECEPTOR PROMOTER JRNL TITL 3 DNA. JRNL REF J.MOL.BIOL. V. 397 278 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20079749 JRNL DOI 10.1016/J.JMB.2010.01.017 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH V.B.AGARKAR,N.D.BABAYEVA,A.RIZZINO,T.H.TAHIROV REMARK 1 TITL PRELIMINARY CRYSTALLOGRAPHIC ANALYSIS OF MOUSE ELF3 REMARK 1 TITL 2 C-TERMINAL DNA-BINDING DOMAIN IN COMPLEX WITH TYPE II REMARK 1 TITL 3 TGF-BETA RECEPTOR PROMOTER DNA REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 65 1261 2009 REMARK 1 REFN ESSN 1744-3091 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1294278.670 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 11365 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) : 0.234 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 585 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1688 REMARK 3 BIN R VALUE (WORKING SET) : 0.4030 REMARK 3 BIN FREE R VALUE : 0.5360 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 91 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.056 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 818 REMARK 3 NUCLEIC ACID ATOMS : 650 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 54 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.90000 REMARK 3 B22 (A**2) : -0.53000 REMARK 3 B33 (A**2) : -0.37000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.34 REMARK 3 ESD FROM SIGMAA (A) : 0.46 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.39 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.61 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.020 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 37.06 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 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3JTG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-SEP-09. REMARK 100 THE DEPOSITION ID IS D_1000055137. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11575 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 53.4500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.39000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE, 0.01 M REMARK 280 MAGNESIUM ACETATE TETRAHYDRATE, 0.05 M SODIUM CACODYLATE REMARK 280 TRIHYDRATE PH 6.5, 25% W/V PEG 8000, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 295K 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 21.33000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.89150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.00250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.89150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.33000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.00250 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 ALA A 269 REMARK 465 PRO A 270 REMARK 465 ARG A 271 REMARK 465 GLY A 367 REMARK 465 GLU A 368 REMARK 465 SER A 369 REMARK 465 ARG A 370 REMARK 465 ASN A 371 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 GLU A 290 47.56 -71.88 REMARK 500 ASN A 297 93.83 -161.84 REMARK 500 REMARK 500 REMARK: NULL DBREF 3JTG A 269 371 UNP Q3UPW2 ELF3_MOUSE 289 391 DBREF 3JTG B 1 16 PDB 3JTG 3JTG 1 16 DBREF 3JTG C 101 116 PDB 3JTG 3JTG 101 116 SEQRES 1 A 103 ALA PRO ARG GLY THR HIS LEU TRP GLU PHE ILE ARG ASP SEQRES 2 A 103 ILE LEU ILE HIS PRO GLU LEU ASN GLU GLY LEU MET LYS SEQRES 3 A 103 TRP GLU ASN ARG HIS GLU GLY VAL PHE LYS PHE LEU ARG SEQRES 4 A 103 SER GLU ALA VAL ALA GLN LEU TRP GLY GLN LYS LYS LYS SEQRES 5 A 103 ASN SER ASN MET THR TYR GLU LYS LEU SER ARG ALA MET SEQRES 6 A 103 ARG TYR TYR TYR LYS ARG GLU ILE LEU GLU ARG VAL ASP SEQRES 7 A 103 GLY ARG ARG LEU VAL TYR LYS PHE GLY LYS ASN SER SER SEQRES 8 A 103 GLY TRP LYS GLU GLU GLU VAL GLY GLU SER ARG ASN SEQRES 1 B 16 DG DA DG DG DA DG DT DT DT DC DC DT DG SEQRES 2 B 16 DT DT DT SEQRES 1 C 16 DC DA DA DA DC DA DG DG DA DA DA DC DT SEQRES 2 C 16 DC DC DT FORMUL 4 HOH *54(H2 O) HELIX 1 1 HIS A 274 ILE A 284 1 11 HELIX 2 2 HIS A 285 ASN A 289 5 5 HELIX 3 3 ARG A 307 LYS A 319 1 13 HELIX 4 4 THR A 325 TYR A 335 1 11 SHEET 1 A 3 MET A 293 ASN A 297 0 SHEET 2 A 3 VAL A 302 PHE A 305 -1 O VAL A 302 N GLU A 296 SHEET 3 A 3 VAL A 351 LYS A 353 -1 O TYR A 352 N PHE A 303 CRYST1 42.660 52.005 99.783 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 0.023441 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019229 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010022 0.00000