Header list of 1bym.pdb file
Complete list - b 16 2 Bytes
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 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
Complete list - b 16 2 Bytes