HEADER DNA BINDING PROTEIN 14-JUL-97 1AOY TITLE N-TERMINAL DOMAIN OF ESCHERICHIA COLI ARGININE REPRESSOR NMR, 23 TITLE 2 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARGININE REPRESSOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 CELL_LINE: BL21; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: X90 (DE3) AND BL21 (DE3) ARG; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: T7; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PET; SOURCE 11 EXPRESSION_SYSTEM_VECTOR: PET3A; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: BL21 KEYWDS DNA-BINDING PROTEIN, EXPRESSION REGULATION, DNA ORGANIZATION, WINGED KEYWDS 2 HELIX, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 23 AUTHOR M.SUNNERHAGEN,M.NILGES,G.OTTING REVDAT 4 10-APR-24 1AOY 1 KEYWDS REVDAT 3 13-JUL-11 1AOY 1 VERSN REVDAT 2 24-FEB-09 1AOY 1 VERSN REVDAT 1 17-SEP-97 1AOY 0 JRNL AUTH M.SUNNERHAGEN,M.NILGES,G.OTTING,J.CAREY JRNL TITL SOLUTION STRUCTURE OF THE DNA-BINDING DOMAIN AND MODEL FOR JRNL TITL 2 THE COMPLEX OF MULTIFUNCTIONAL HEXAMERIC ARGININE REPRESSOR JRNL TITL 3 WITH DNA. JRNL REF NAT.STRUCT.BIOL. V. 4 819 1997 JRNL REFN ISSN 1072-8368 JRNL PMID 9334747 JRNL DOI 10.1038/NSB1097-819 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER (MODIFICATIONS: NILGES) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES WERE CALCULATED WITH A REMARK 3 MODIFIED VERSION OF X-PLOR WITH A SIMULATED ANNEALING PROTOCOL. REMARK 3 AN AUTOMATED PROCEDURE (ARIA) WAS USED TO AUTOMATICALLY REMARK 3 CALIBRATE, SELECT AND ASSIGN PEAK LISTS FROM HOMONUCLEAR H2O AND REMARK 3 D2O AND N15-EDITED 3D NOESY SPECTRA. 20 STRUCTURES WERE REMARK 3 ITERATIVELY REFINED, AND THE NOE DATA RE-ASSIGNED ON THE BASIS REMARK 3 OF THE 7 LOWEST ENERGY STRUCTURES IN EACH ITERATION. THE REMARK 3 AUTOMATICALLY GENERATED ASSIGNMENTS WERE CHECKED MANUALLY AND REMARK 3 CORRECTED IF NECESSARY. THE FINAL LIST OF RESTRAINTS CONTAINED REMARK 3 2008 UNAMBIGUOUS RESTRAINTS AND 280 AMBIGUOUS RESTRAINTS WITH REMARK 3 MAXIMALLY 5 ASSIGNMENT POSSIBILITIES. WITH THE FINAL RESTRAINT REMARK 3 LIST, A TOTAL OF 75 STRUCTURES WERE CALCULATED. THE 23 REMARK 3 STRUCTURES WITH THE LOWEST TOTAL ENERGY WERE REFINED IN AN REMARK 3 EXPLICIT SHELL OF WATER. THE STRUCTURAL STATISTICS GIVEN BELOW REMARK 3 ARE FOR THE STRUCTURES AFTER THE REFINEMENT IN WATER. REFINEMENT REMARK 3 DETAILS CAN BE FOUND IN THE JRNL REFERENCE ABOVE. THE 23 REMARK 3 DEPOSITED STRUCTURES ARE IN ORDER OF RISING RESTRAINT ENERGY REMARK 3 AFTER WATER REFINEMENT. NOES TO ALL PROCHIRAL GROUPS WERE REMARK 3 TREATED WITH A FLOATING CHIRALITY APPROACH THAT ALLOWS EXPLICIT REMARK 3 SWAPPING OF PROTONS AND METHYL GROUPS; THE ATOM NAMES IN THE REMARK 3 COORDINATE ENTRY HAVE BEEN RENAMED TO BE CONSISTENT WITH REMARK 3 STANDARD IUB/IUPAC CONVENTION. REMARK 4 REMARK 4 1AOY COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171079. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 301 REMARK 210 PH : 5.8 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2QF-COSY; 3QF-COSY; E-COSY; REMARK 210 CLEAN TOCSY; NOESY; HNHB; 13C- REMARK 210 HMBC; TOCSY-15N-HSQC; NOESY-15N- REMARK 210 HSQC; 3D HNCO REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 75 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 23 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL 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 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 SER A 3 77.00 -102.32 REMARK 500 1 GLN A 7 37.37 -81.93 REMARK 500 1 GLU A 21 72.75 61.55 REMARK 500 1 LYS A 22 -41.88 -140.27 REMARK 500 1 PRO A 70 -154.38 -73.66 REMARK 500 1 GLU A 72 106.07 -45.80 REMARK 500 1 THR A 77 -37.35 -164.85 REMARK 500 2 ARG A 2 43.14 -100.75 REMARK 500 2 SER A 3 -59.26 72.47 REMARK 500 2 LYS A 6 98.82 -69.57 REMARK 500 2 GLU A 8 36.94 -80.92 REMARK 500 2 GLU A 21 80.01 61.74 REMARK 500 2 LYS A 22 -53.00 -142.15 REMARK 500 2 ASN A 40 54.88 92.77 REMARK 500 2 LYS A 62 32.40 -99.73 REMARK 500 2 PRO A 70 -140.27 -67.68 REMARK 500 2 GLU A 72 109.90 -58.21 REMARK 500 3 ARG A 2 -95.10 -75.52 REMARK 500 3 GLU A 21 63.54 61.59 REMARK 500 3 ASN A 40 66.46 -116.44 REMARK 500 3 GLU A 72 108.40 -31.15 REMARK 500 3 THR A 77 55.82 -161.10 REMARK 500 4 ARG A 2 62.51 61.32 REMARK 500 4 SER A 3 75.81 -118.11 REMARK 500 4 GLU A 21 81.00 63.64 REMARK 500 4 LYS A 22 -55.74 -139.18 REMARK 500 4 ASN A 60 -154.96 -83.38 REMARK 500 4 PRO A 70 -159.13 -66.09 REMARK 500 4 GLU A 72 104.69 -46.70 REMARK 500 4 LEU A 73 47.43 -83.87 REMARK 500 5 SER A 3 88.87 66.34 REMARK 500 5 ALA A 5 59.25 -155.55 REMARK 500 5 GLU A 21 72.63 61.95 REMARK 500 5 LYS A 22 -53.32 -137.76 REMARK 500 5 ASN A 40 50.76 94.95 REMARK 500 5 PRO A 70 -149.46 -70.53 REMARK 500 5 GLU A 72 128.18 -39.87 REMARK 500 5 PRO A 76 27.05 -71.34 REMARK 500 6 ALA A 5 78.11 -159.80 REMARK 500 6 GLU A 21 66.97 64.58 REMARK 500 6 LYS A 22 -53.75 -130.12 REMARK 500 6 ASN A 40 32.25 -99.26 REMARK 500 6 ALA A 71 101.12 -49.67 REMARK 500 6 GLU A 72 75.25 52.33 REMARK 500 6 THR A 77 -158.74 -152.90 REMARK 500 7 GLN A 7 33.62 -76.72 REMARK 500 7 LYS A 22 38.72 -142.00 REMARK 500 7 PRO A 70 -146.04 -66.78 REMARK 500 7 ALA A 71 -152.13 -75.41 REMARK 500 7 THR A 77 21.52 -78.12 REMARK 500 REMARK 500 THIS ENTRY HAS 171 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1AOY A 1 78 UNP P0A6D0 ARGR_ECOLI 1 78 SEQRES 1 A 78 MET ARG SER SER ALA LYS GLN GLU GLU LEU VAL LYS ALA SEQRES 2 A 78 PHE LYS ALA LEU LEU LYS GLU GLU LYS PHE SER SER GLN SEQRES 3 A 78 GLY GLU ILE VAL ALA ALA LEU GLN GLU GLN GLY PHE ASP SEQRES 4 A 78 ASN ILE ASN GLN SER LYS VAL SER ARG MET LEU THR LYS SEQRES 5 A 78 PHE GLY ALA VAL ARG THR ARG ASN ALA LYS MET GLU MET SEQRES 6 A 78 VAL TYR CYS LEU PRO ALA GLU LEU GLY VAL PRO THR THR HELIX 1 1 LEU A 10 LYS A 19 1 10 HELIX 2 2 GLN A 26 GLN A 36 1 11 HELIX 3 3 GLN A 43 PHE A 53 1 11 SHEET 1 A 2 ALA A 55 ARG A 59 0 SHEET 2 A 2 MET A 65 LEU A 69 -1 N CYS A 68 O VAL A 56 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