PDB Short entry for 1DUX HEADER TRANSCRIPTION/DNA 19-JAN-00 1DUX TITLE ELK-1/DNA STRUCTURE REVEALS HOW RESIDUES DISTAL FROM DNA-BINDING TITLE 2 SURFACE AFFECT DNA-RECOGNITION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*TP*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP*T)-3'); COMPND 3 CHAIN: A, D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*AP*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP*A)-3'); COMPND 7 CHAIN: B, E; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: ETS-DOMAIN PROTEIN ELK-1; COMPND 11 CHAIN: C, F; COMPND 12 FRAGMENT: RESIDUES 1-94; COMPND 13 SYNONYM: TRANSFORMING PROTEIN ELK-1, ELK1, MEMBER OF ETS ONCOGENE COMPND 14 FAMILY; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PRSETA KEYWDS ETS-DOMAIN, DNA-BINDING DOMAIN, WINGED HELIX-TURN-HELIX, DNA-BINDING KEYWDS 2 SPECIFICITY, TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.MO,B.VAESSEN,K.JOHNSTON,R.MARMORSTEIN REVDAT 3 07-FEB-24 1DUX 1 REMARK REVDAT 2 24-FEB-09 1DUX 1 VERSN REVDAT 1 17-APR-00 1DUX 0 JRNL AUTH Y.MO,B.VAESSEN,K.JOHNSTON,R.MARMORSTEIN JRNL TITL STRUCTURE OF THE ELK-1-DNA COMPLEX REVEALS HOW DNA-DISTAL JRNL TITL 2 RESIDUES AFFECT ETS DOMAIN RECOGNITION OF DNA. JRNL REF NAT.STRUCT.BIOL. V. 7 292 2000 JRNL REFN ISSN 1072-8368 JRNL PMID 10742173 JRNL DOI 10.1038/74055 REMARK 2 REMARK 2 RESOLUTION. 2.10 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 17831 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) : 0.202 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1827 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1458 REMARK 3 NUCLEIC ACID ATOMS : 1054 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 225 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.50 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.089 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DUX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JAN-00. REMARK 100 THE DEPOSITION ID IS D_1000010391. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-98; 14-JUL-98 REMARK 200 TEMPERATURE (KELVIN) : 110; 110 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : NSLS; NSLS REMARK 200 BEAMLINE : X4A; X8C REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791; 0.98165 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV; MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17831 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 27.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.01 REMARK 200 R MERGE FOR SHELL (I) : 0.09200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM SODIUM CACODYLATE, 10% PEG 2000, REMARK 280 100 MM MGCL2, 100 MM NACL, 3 MM ZNCL2, PH 5.6, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 70.26150 REMARK 290 SMTRY3 2 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D, E, C, 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 MET C 1 REMARK 465 ASP C 2 REMARK 465 PRO C 3 REMARK 465 SER C 4 REMARK 465 VAL C 91 REMARK 465 ALA C 92 REMARK 465 GLY C 93 REMARK 465 CYS C 94 REMARK 465 MET F 1 REMARK 465 ASP F 2 REMARK 465 PRO F 3 REMARK 465 SER F 4 REMARK 465 VAL F 91 REMARK 465 ALA F 92 REMARK 465 GLY F 93 REMARK 465 CYS F 94 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 TYR C 88 117.21 -23.26 REMARK 500 PRO C 89 75.54 -57.61 REMARK 500 PRO F 89 -138.62 -90.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DT B 5 0.07 SIDE CHAIN REMARK 500 DT E 5 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1DUX C 1 94 UNP P19419 ELK1_HUMAN 1 94 DBREF 1DUX F 1 94 UNP P19419 ELK1_HUMAN 1 94 DBREF 1DUX A 1 13 PDB 1DUX 1DUX 1 13 DBREF 1DUX B 1 13 PDB 1DUX 1DUX 1 13 DBREF 1DUX D 1 13 PDB 1DUX 1DUX 1 13 DBREF 1DUX E 1 13 PDB 1DUX 1DUX 1 13 SEQRES 1 A 13 DT DG DA DC DC DG DG DA DA DG DT DG DT SEQRES 1 B 13 DA DC DA DC DT DT DC DC DG DG DT DC DA SEQRES 1 D 13 DT DG DA DC DC DG DG DA DA DG DT DG DT SEQRES 1 E 13 DA DC DA DC DT DT DC DC DG DG DT DC DA SEQRES 1 C 94 MET ASP PRO SER VAL THR LEU TRP GLN PHE LEU LEU GLN SEQRES 2 C 94 LEU LEU ARG GLU GLN GLY ASN GLY HIS ILE ILE SER TRP SEQRES 3 C 94 THR SER ARG ASP GLY GLY GLU PHE LYS LEU VAL ASP ALA SEQRES 4 C 94 GLU GLU VAL ALA ARG LEU TRP GLY LEU ARG LYS ASN LYS SEQRES 5 C 94 THR ASN MET ASN TYR ASP LYS LEU SER ARG ALA LEU ARG SEQRES 6 C 94 TYR TYR TYR ASP LYS ASN ILE ILE ARG LYS VAL SER GLY SEQRES 7 C 94 GLN LYS PHE VAL TYR LYS PHE VAL SER TYR PRO GLU VAL SEQRES 8 C 94 ALA GLY CYS SEQRES 1 F 94 MET ASP PRO SER VAL THR LEU TRP GLN PHE LEU LEU GLN SEQRES 2 F 94 LEU LEU ARG GLU GLN GLY ASN GLY HIS ILE ILE SER TRP SEQRES 3 F 94 THR SER ARG ASP GLY GLY GLU PHE LYS LEU VAL ASP ALA SEQRES 4 F 94 GLU GLU VAL ALA ARG LEU TRP GLY LEU ARG LYS ASN LYS SEQRES 5 F 94 THR ASN MET ASN TYR ASP LYS LEU SER ARG ALA LEU ARG SEQRES 6 F 94 TYR TYR TYR ASP LYS ASN ILE ILE ARG LYS VAL SER GLY SEQRES 7 F 94 GLN LYS PHE VAL TYR LYS PHE VAL SER TYR PRO GLU VAL SEQRES 8 F 94 ALA GLY CYS FORMUL 7 HOH *225(H2 O) HELIX 1 1 THR C 6 GLN C 18 1 13 HELIX 2 2 ASP C 38 ARG C 49 1 12 HELIX 3 3 ASN C 56 TYR C 68 1 13 HELIX 4 4 ASP C 69 ASN C 71 5 3 HELIX 5 5 THR F 6 GLN F 18 1 13 HELIX 6 6 ASP F 38 LYS F 50 1 13 HELIX 7 7 ASN F 56 TYR F 68 1 13 SHEET 1 A 4 SER C 25 SER C 28 0 SHEET 2 A 4 GLU C 33 LYS C 35 -1 O GLU C 33 N THR C 27 SHEET 3 A 4 VAL C 82 PHE C 85 -1 N TYR C 83 O PHE C 34 SHEET 4 A 4 ILE C 73 LYS C 75 -1 O ARG C 74 N LYS C 84 SHEET 1 B 4 SER F 25 SER F 28 0 SHEET 2 B 4 GLU F 33 LYS F 35 -1 O GLU F 33 N THR F 27 SHEET 3 B 4 VAL F 82 PHE F 85 -1 N TYR F 83 O PHE F 34 SHEET 4 B 4 ILE F 73 LYS F 75 -1 O ARG F 74 N LYS F 84 CRYST1 33.245 140.523 38.620 90.00 115.52 90.00 P 1 21 1 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 0.030080 0.000000 0.014360 0.00000 SCALE2 0.000000 0.007116 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028693 0.00000