PDB Short entry for 1SRS HEADER TRANSCRIPTION/DNA 28-JUL-95 1SRS TITLE SERUM RESPONSE FACTOR (SRF) CORE COMPLEXED WITH SPECIFIC SRE DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*CP*(5IU) COMPND 3 P*TP*CP*CP*TP*AP*AP*TP*TP*AP*GP*GP*CP*CP*AP*TP*G)-3'); COMPND 4 CHAIN: W; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'- COMPND 8 D(*CP*CP*AP*TP*GP*GP*CP*CP*TP*AP*AP*TP*TP*AP*GP*GP*A P*AP*G)-3'); COMPND 9 CHAIN: C; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: PROTEIN (SERUM RESPONSE FACTOR (SRF)); COMPND 13 CHAIN: A, B; COMPND 14 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 GENE: SRF CORE (RESIDUES 132-223); SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 12 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PET3A; SOURCE 14 EXPRESSION_SYSTEM_GENE: SRF CORE (RESIDUES 132-223) KEYWDS TRANSCRIPTION REGULATION, MADS-DOMAIN, COMPLEX (DNA BINDING PROTEIN- KEYWDS 2 DNA), TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.PELLEGRINI,S.TAN,T.J.RICHMOND REVDAT 3 14-FEB-24 1SRS 1 LINK REVDAT 2 24-FEB-09 1SRS 1 VERSN REVDAT 1 28-JUL-95 1SRS 0 JRNL AUTH L.PELLEGRINI,S.TAN,T.J.RICHMOND JRNL TITL STRUCTURE OF SERUM RESPONSE FACTOR CORE BOUND TO DNA. JRNL REF NATURE V. 376 490 1995 JRNL REFN ISSN 0028-0836 JRNL PMID 7637780 JRNL DOI 10.1038/376490A0 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 7162 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 1304 REMARK 3 NUCLEIC ACID ATOMS : 770 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 0.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 35.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.870 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 ; 1.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; 1.500 REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; 1.500 REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; 2.000 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 1SRS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000176488. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 277.00 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7629 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.50, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293.00K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 38.44000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 53.42000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 53.42000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 57.66000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 53.42000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 53.42000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 19.22000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 53.42000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 53.42000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 57.66000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 53.42000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 53.42000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 19.22000 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 38.44000 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 300 REMARK: THERE IS ONE COMPLEX PER ASYMMETRIC UNIT CONSISTING OF TWO REMARK 300 IDENTICAL POLYPEPTIDE CHAINS LABELLED *A* AND *B* AND TWO REMARK 300 DNA CHAINS LABELLED *W* AND *C*. 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: W, C, 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 SER A 132 REMARK 465 GLY A 133 REMARK 465 ALA A 134 REMARK 465 LYS A 135 REMARK 465 PRO A 136 REMARK 465 GLY A 137 REMARK 465 LYS A 138 REMARK 465 LYS A 139 REMARK 465 SER B 132 REMARK 465 GLY B 133 REMARK 465 ALA B 134 REMARK 465 LYS B 135 REMARK 465 PRO B 136 REMARK 465 GLY B 137 REMARK 465 LYS B 138 REMARK 465 LYS B 139 REMARK 465 ASN B 220 REMARK 465 SER B 221 REMARK 465 PRO B 222 REMARK 465 ASP B 223 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 MET A 148 96.83 -60.10 REMARK 500 LYS B 145 97.65 -69.47 REMARK 500 MET B 148 95.47 -61.66 REMARK 500 ARG B 200 -70.53 -32.85 REMARK 500 REMARK 500 REMARK: NULL DBREF 1SRS A 132 223 UNP P11831 SRF_HUMAN 87 178 DBREF 1SRS B 132 223 UNP P11831 SRF_HUMAN 87 178 DBREF 1SRS W -9 10 PDB 1SRS 1SRS -9 10 DBREF 1SRS C 11 -8 PDB 1SRS 1SRS 11 -8 SEQRES 1 W 19 DC DC 5IU DT DC DC DT DA DA DT DT DA DG SEQRES 2 W 19 DG DC DC DA DT DG SEQRES 1 C 19 DC DC DA DT DG DG DC DC DT DA DA DT DT SEQRES 2 C 19 DA DG DG DA DA DG SEQRES 1 A 92 SER GLY ALA LYS PRO GLY LYS LYS THR ARG GLY ARG VAL SEQRES 2 A 92 LYS ILE LYS MET GLU PHE ILE ASP ASN LYS LEU ARG ARG SEQRES 3 A 92 TYR THR THR PHE SER LYS ARG LYS THR GLY ILE MET LYS SEQRES 4 A 92 LYS ALA TYR GLU LEU SER THR LEU THR GLY THR GLN VAL SEQRES 5 A 92 LEU LEU LEU VAL ALA SER GLU THR GLY HIS VAL TYR THR SEQRES 6 A 92 PHE ALA THR ARG LYS LEU GLN PRO MET ILE THR SER GLU SEQRES 7 A 92 THR GLY LYS ALA LEU ILE GLN THR CYS LEU ASN SER PRO SEQRES 8 A 92 ASP SEQRES 1 B 92 SER GLY ALA LYS PRO GLY LYS LYS THR ARG GLY ARG VAL SEQRES 2 B 92 LYS ILE LYS MET GLU PHE ILE ASP ASN LYS LEU ARG ARG SEQRES 3 B 92 TYR THR THR PHE SER LYS ARG LYS THR GLY ILE MET LYS SEQRES 4 B 92 LYS ALA TYR GLU LEU SER THR LEU THR GLY THR GLN VAL SEQRES 5 B 92 LEU LEU LEU VAL ALA SER GLU THR GLY HIS VAL TYR THR SEQRES 6 B 92 PHE ALA THR ARG LYS LEU GLN PRO MET ILE THR SER GLU SEQRES 7 B 92 THR GLY LYS ALA LEU ILE GLN THR CYS LEU ASN SER PRO SEQRES 8 B 92 ASP MODRES 1SRS 5IU W -7 DU 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE HET 5IU W -7 20 HETNAM 5IU 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE FORMUL 1 5IU C9 H12 I N2 O8 P HELIX 1 1 ASN A 153 THR A 179 1 27 HELIX 2 2 GLU A 209 LEU A 219 1 11 HELIX 3 3 ASN B 153 THR B 179 1 27 HELIX 4 4 GLU B 209 LEU B 219 1 11 SHEET 1 A 4 VAL A 194 ALA A 198 0 SHEET 2 A 4 GLN A 182 ALA A 188 -1 N VAL A 187 O TYR A 195 SHEET 3 A 4 GLN B 182 ALA B 188 -1 N ALA B 188 O GLN A 182 SHEET 4 A 4 VAL B 194 ALA B 198 -1 N PHE B 197 O LEU B 185 LINK O3' DC W -8 P 5IU W -7 1555 1555 1.60 LINK O3' 5IU W -7 P DT W -6 1555 1555 1.60 CRYST1 106.840 106.840 76.880 90.00 90.00 90.00 P 43 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 0.009360 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009360 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013007 0.00000