HEADER GENE REGULATION 17-OCT-98 1BYM TITLE SOLUTION STRUCTURES OF THE C-TERMINAL DOMAIN OF DIPHTHERIA TOXIN TITLE 2 REPRESSOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (DIPHTHERIA TOXIN REPRESSOR); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 130-226; COMPND 5 SYNONYM: DTXR(130-226); COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CORYNEBACTERIUM DIPHTHERIAE; SOURCE 3 ORGANISM_TAXID: 1717; SOURCE 4 GENE: DTXR; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: HMS-174; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PQE-31; SOURCE 9 OTHER_DETAILS: SWS P33120 KEYWDS REPRESSOR, DTXR, C-TERMINAL DOMAIN, PROKARYOTIC SH3 DOMAIN, KEYWDS 2 TRANSCRIPTION REGULATION, PEPTIDE-BINDING, GENE REGULATION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.WANG,G.P.WYLIE,P.D.TWIGG,D.L.D.CASPAR,J.R.MURPHY,T.M.LOGAN REVDAT 6 22-MAY-24 1BYM 1 REMARK REVDAT 5 16-FEB-22 1BYM 1 REMARK REVDAT 4 24-FEB-09 1BYM 1 VERSN REVDAT 3 01-APR-03 1BYM 1 JRNL REVDAT 2 22-DEC-99 1BYM 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 21-OCT-98 1BYM 0 JRNL AUTH G.WANG,G.P.WYLIE,P.D.TWIGG,D.L.CASPAR,J.R.MURPHY,T.M.LOGAN JRNL TITL SOLUTION STRUCTURE AND PEPTIDE BINDING STUDIES OF THE JRNL TITL 2 C-TERMINAL SRC HOMOLOGY 3-LIKE DOMAIN OF THE DIPHTHERIA JRNL TITL 3 TOXIN REPRESSOR PROTEIN. JRNL REF PROC.NATL.ACAD.SCI.USA V. 96 6119 1999 JRNL REFN ISSN 0027-8424 JRNL PMID 10339551 JRNL DOI 10.1073/PNAS.96.11.6119 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE. REMARK 4 REMARK 4 1BYM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000008149. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HSQC; HNCACB; CBCA(CO)NH; HNCO; REMARK 210 H(C)(CO)NH-TOCSY; HCCH-TOCSY; REMARK 210 TOCSY-HSQC; (15N,1H,1H)NOESY- REMARK 210 HSQC; (13C,1H,1H)HMQC-NOESY; REMARK 210 (13C,13C,1H)HMQC-NOESY; (1H,1H) REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 720 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR REMARK 210 METHOD USED : DISTANCE GEOMETRY AND SIMULATED REMARK 210 ANNEALING CALCULATIONS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : NO NOE DISTANCE VIOLATION REMARK 210 GREATER THAN 0.35 A, NO DIHEDRAL REMARK 210 ANGLE RESTRAINT VIOLATION REMARK 210 GREATER THAN 5 DEG, RMS REMARK 210 DIFFERENCE FOR BOND DEVIATIONS REMARK 210 FROM IDEALITY LESS THAN 0.01 A, REMARK 210 RMS DIFFERENCE FOR ANGLE REMARK 210 DEVIATIONS FROM IDEALITY LESS REMARK 210 THAN 2 DEG, LOWEST TOTAL ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 20 REMARK 210 REMARK 210 REMARK: IONIC_STRENGTH: NULL PRESSURE: NULL SOLVENT SYSTEM: REMARK 210 H2O/D2O (9:1, V/V) REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O GLU A 194 H SER A 205 1.43 REMARK 500 H ARG A 198 O HIS A 201 1.51 REMARK 500 O ARG A 151 H ILE A 153 1.51 REMARK 500 O LEU A 217 HG1 THR A 220 1.52 REMARK 500 HH12 ARG A 161 O ILE A 195 1.57 REMARK 500 O VAL A 189 N SER A 191 1.99 REMARK 500 O VAL A 163 O VAL A 193 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 1 PRO A 133 -168.20 -72.99 REMARK 500 1 ASP A 136 46.43 -151.86 REMARK 500 1 VAL A 140 100.92 55.12 REMARK 500 1 ASN A 142 -169.17 51.33 REMARK 500 1 ASP A 144 -167.74 58.38 REMARK 500 1 ALA A 145 84.83 45.00 REMARK 500 1 ARG A 151 135.99 58.41 REMARK 500 1 VAL A 152 56.22 -65.84 REMARK 500 1 ILE A 153 -37.10 -158.92 REMARK 500 1 SER A 158 -39.62 -38.62 REMARK 500 1 ARG A 161 -135.19 -63.37 REMARK 500 1 VAL A 163 -150.43 -123.74 REMARK 500 1 ARG A 164 155.41 179.48 REMARK 500 1 GLN A 167 114.06 -177.04 REMARK 500 1 ASN A 169 172.05 -44.86 REMARK 500 1 GLU A 170 92.04 -166.68 REMARK 500 1 VAL A 174 90.15 179.76 REMARK 500 1 THR A 176 -82.93 -138.07 REMARK 500 1 ASP A 177 -159.36 70.96 REMARK 500 1 ILE A 187 -72.99 -138.60 REMARK 500 1 ARG A 188 157.17 72.46 REMARK 500 1 VAL A 189 36.52 33.17 REMARK 500 1 SER A 191 -144.38 38.29 REMARK 500 1 VAL A 193 -137.63 -159.27 REMARK 500 1 ASP A 199 81.67 40.72 REMARK 500 1 ASN A 207 77.42 -59.63 REMARK 500 1 LYS A 209 124.64 -174.06 REMARK 500 1 LEU A 213 -160.01 -76.93 REMARK 500 1 HIS A 219 49.99 -103.50 REMARK 500 1 THR A 220 -61.59 -133.74 REMARK 500 2 PRO A 133 -164.52 -73.08 REMARK 500 2 ASP A 136 42.25 -89.62 REMARK 500 2 VAL A 140 -156.63 -117.96 REMARK 500 2 SER A 143 -142.30 -166.25 REMARK 500 2 ASP A 144 -163.36 54.16 REMARK 500 2 ALA A 147 158.35 62.76 REMARK 500 2 ARG A 151 118.15 61.00 REMARK 500 2 VAL A 152 165.95 -42.82 REMARK 500 2 ILE A 153 -20.68 72.17 REMARK 500 2 ARG A 164 147.61 -173.54 REMARK 500 2 GLU A 170 123.05 172.68 REMARK 500 2 PHE A 172 -138.67 25.06 REMARK 500 2 GLN A 173 -145.94 -105.04 REMARK 500 2 THR A 176 -84.48 -148.29 REMARK 500 2 ASP A 177 -139.16 70.09 REMARK 500 2 ARG A 188 168.04 53.22 REMARK 500 2 VAL A 189 37.67 31.46 REMARK 500 2 SER A 191 -153.24 41.52 REMARK 500 2 VAL A 193 -131.97 -159.80 REMARK 500 2 ASP A 197 123.28 -39.39 REMARK 500 REMARK 500 THIS ENTRY HAS 531 RAMACHANDRAN OUTLIERS. 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 1 ARG A 151 0.32 SIDE CHAIN REMARK 500 1 ARG A 161 0.18 SIDE CHAIN REMARK 500 1 ARG A 164 0.19 SIDE CHAIN REMARK 500 1 ARG A 188 0.19 SIDE CHAIN REMARK 500 1 ARG A 198 0.32 SIDE CHAIN REMARK 500 1 ARG A 222 0.14 SIDE CHAIN REMARK 500 2 ARG A 151 0.16 SIDE CHAIN REMARK 500 2 ARG A 161 0.29 SIDE CHAIN REMARK 500 2 ARG A 164 0.22 SIDE CHAIN REMARK 500 2 ARG A 188 0.28 SIDE CHAIN REMARK 500 2 ARG A 198 0.18 SIDE CHAIN REMARK 500 2 ARG A 222 0.19 SIDE CHAIN REMARK 500 3 ARG A 151 0.30 SIDE CHAIN REMARK 500 3 ARG A 161 0.27 SIDE CHAIN REMARK 500 3 ARG A 164 0.17 SIDE CHAIN REMARK 500 3 ARG A 188 0.30 SIDE CHAIN REMARK 500 3 ARG A 198 0.12 SIDE CHAIN REMARK 500 3 ARG A 222 0.23 SIDE CHAIN REMARK 500 4 ARG A 151 0.22 SIDE CHAIN REMARK 500 4 ARG A 161 0.10 SIDE CHAIN REMARK 500 4 ARG A 164 0.31 SIDE CHAIN REMARK 500 4 ARG A 188 0.14 SIDE CHAIN REMARK 500 4 ARG A 198 0.25 SIDE CHAIN REMARK 500 4 ARG A 222 0.23 SIDE CHAIN REMARK 500 5 ARG A 151 0.31 SIDE CHAIN REMARK 500 5 ARG A 161 0.19 SIDE CHAIN REMARK 500 5 ARG A 164 0.28 SIDE CHAIN REMARK 500 5 ARG A 188 0.13 SIDE CHAIN REMARK 500 5 ARG A 198 0.29 SIDE CHAIN REMARK 500 5 ARG A 222 0.21 SIDE CHAIN REMARK 500 6 ARG A 151 0.27 SIDE CHAIN REMARK 500 6 ARG A 161 0.30 SIDE CHAIN REMARK 500 6 ARG A 164 0.26 SIDE CHAIN REMARK 500 6 ARG A 188 0.30 SIDE CHAIN REMARK 500 6 ARG A 198 0.20 SIDE CHAIN REMARK 500 6 ARG A 222 0.13 SIDE CHAIN REMARK 500 7 ARG A 151 0.28 SIDE CHAIN REMARK 500 7 ARG A 161 0.32 SIDE CHAIN REMARK 500 7 ARG A 164 0.24 SIDE CHAIN REMARK 500 7 ARG A 188 0.20 SIDE CHAIN REMARK 500 7 ARG A 198 0.29 SIDE CHAIN REMARK 500 7 ARG A 222 0.24 SIDE CHAIN REMARK 500 8 ARG A 151 0.08 SIDE CHAIN REMARK 500 8 ARG A 161 0.18 SIDE CHAIN REMARK 500 8 ARG A 164 0.09 SIDE CHAIN REMARK 500 8 ARG A 188 0.29 SIDE CHAIN REMARK 500 8 ARG A 198 0.21 SIDE CHAIN REMARK 500 8 ARG A 222 0.30 SIDE CHAIN REMARK 500 9 ARG A 151 0.25 SIDE CHAIN REMARK 500 9 ARG A 161 0.27 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 117 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1BYM A 130 226 UNP P33120 DTXR_CORDI 130 226 SEQRES 1 A 97 ASN PRO ILE PRO GLY LEU ASP GLU LEU GLY VAL GLY ASN SEQRES 2 A 97 SER ASP ALA ALA ALA PRO GLY THR ARG VAL ILE ASP ALA SEQRES 3 A 97 ALA THR SER MET PRO ARG LYS VAL ARG ILE VAL GLN ILE SEQRES 4 A 97 ASN GLU ILE PHE GLN VAL GLU THR ASP GLN PHE THR GLN SEQRES 5 A 97 LEU LEU ASP ALA ASP ILE ARG VAL GLY SER GLU VAL GLU SEQRES 6 A 97 ILE VAL ASP ARG ASP GLY HIS ILE THR LEU SER HIS ASN SEQRES 7 A 97 GLY LYS ASP VAL GLU LEU LEU ASP ASP LEU ALA HIS THR SEQRES 8 A 97 ILE ARG ILE GLU GLU LEU HELIX 1 1 ARG A 151 ASP A 154 1 4 HELIX 2 2 ASP A 177 ALA A 185 5 9 HELIX 3 3 ASP A 215 ALA A 218 1 4 SHEET 1 A 3 VAL A 193 ARG A 198 0 SHEET 2 A 3 HIS A 201 HIS A 206 -1 N SER A 205 O GLU A 194 SHEET 3 A 3 LYS A 209 VAL A 211 -1 N VAL A 211 O LEU A 204 SHEET 1 B 2 VAL A 163 GLN A 167 0 SHEET 2 B 2 ARG A 222 GLU A 225 -1 N GLU A 224 O ARG A 164 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1