HEADER GENE REGULATION 27-JUN-99 1QTG TITLE AVERAGED NMR MODEL OF SWITCH ARC, A DOUBLE MUTANT OF ARC TITLE 2 REPRESSOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARC REPRESSOR; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE P22; SOURCE 3 ORGANISM_TAXID: 10754; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET800-SWITCH_ARC; SOURCE 8 OTHER_DETAILS: MUTATED SYNTHETIC ARC GENE KEYWDS BETA-SHEET, RIGHT-HANDED HELIX, STRUCTURAL CHANGE, GENE KEYWDS 2 REGULATION EXPDTA SOLUTION NMR AUTHOR M.H.J.CORDES,N.P.WALSH,C.J.MCKNIGHT,R.T.SAUER REVDAT 3 24-FEB-09 1QTG 1 VERSN REVDAT 2 01-APR-03 1QTG 1 JRNL REVDAT 1 12-JUL-99 1QTG 0 JRNL AUTH M.H.CORDES,N.P.WALSH,C.J.MCKNIGHT,R.T.SAUER JRNL TITL EVOLUTION OF A PROTEIN FOLD IN VITRO. JRNL REF SCIENCE V. 284 325 1999 JRNL REFN ISSN 0036-8075 JRNL PMID 10195898 JRNL DOI 10.1126/SCIENCE.284.5412.325 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: GENERATION OF THIS MODEL OF THE REMARK 3 SWITCH ARC MUTANT INVOLVED A COMBINATION OF EXPERIMENTAL AND REMARK 3 SIMU LATED DISTANCE RESTRAINTS. FOR RESIDUES 7-14, 81 NOE REMARK 3 CROSSPEAKS WERE OBTAINED FROM A 50-MS 2D NOES Y SPECTRUM AND REMARK 3 WERE TRANSLATED INTO STRONG (1.8-2.8 A), MEDIUM (1.8-3.3 A), REMARK 3 MEDIUM-WEAK (1.8-3.8 A ) AND WEAK (1.8-4.3 A) DISTANCE REMARK 3 RESTRAINTS.18 ADDITIONAL CROSSPEAKS WERE OBTAINED FROM A 150- REMARK 3 MS 3D NOESY SPECTRUM AND WERE ASSIGNED LOOSER RESTRAINTS (1.8 REMARK 3 TO 4.0 A OR 1.8 TO 6.0 A)BECAUSE OF THE L ONGER MIXING TIME REMARK 3 USED IN THIS EXPERIMENT. TO SIMULATE THE STRUCTURE OF RESIDUES REMARK 3 14 TO 53 (RESIDUE 14 WAS DESCRIBED BY BOTH ACTUAL AND COMPUTED REMARK 3 RESTRAINTS), A LIST OF 1635 DISTANCES WAS GENERATED BETWEEN REMARK 3 PAIRS OF HEAVY ATOMS WITHIN 4 A OF EACH OTHER IN THE WILD-TYPE REMARK 3 ARC CRYSTAL STRUCTURE, AND THE INTERATOMIC DISTANCES WERE REMARK 3 CONSTRAINED TO BE WITHIN + OR - 1.0 A OF THIS VALUE. 28 REMARK 3 INITIAL STR UCTURES WITH RANDOM CONFIGURATIONS FOR RESIDUES 1 REMARK 3 TO 13 WERE GENERATED BY PERFORMING A SET OF CALC ULATIONS WITH REMARK 3 ONLY THE SIMULATED RESTRAINTS FOR RESIDUES 14 TO 53. THEN, 28 REMARK 3 MODEL STRUCTURES WERE GENERATED BY INCLUDING THE EXPERIMENTAL REMARK 3 RESTRAINTS FOR RESIDUES 7 TO 14. NO RESTRAINTS WERE USED F OR REMARK 3 RESIDUES 1 TO 6, WHICH APPEAR TO BE DISORDERED. AMBIGUITIES IN REMARK 3 INTRA- AND INTERMOLECULAR NOE AS SIGNMENT RESULTING FROM ARC'S REMARK 3 TWOFOLD SYMMETRY WERE RESOLVED COMPUTATIONALLY AS DESCRIBED REMARK 3 (M. NILG ES, PROTEIN STRUCT. FUNCT. GENET. 17, 297 (1993).19 REMARK 3 OF 28 STRUCTURES WERE ACCEPTED WITH NO NOE VIO LATIONS GREATER REMARK 3 THAN 0.3 A. THE FIVE STRUCTURES WITH THE HIGHEST ENERGY, WHICH REMARK 3 ALSO CONTAINED BACK BONE DIHEDRAL ANGLES IN DISALLOWED REGIONS REMARK 3 OF RAMACHANDRAN SPACE, WERE DISCARDED. THE REMAINING 14 REMARK 3 STRUCTURES, WHICH HAD PAIRWISE RMSD'S OF 0.6 A (BACKBONE) AND REMARK 3 1.6 A (HEAVY), WERE USED TO GENERAT E A MINIMIZED AVERAGE REMARK 3 MODEL. REMARK 4 REMARK 4 1QTG COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUN-99. REMARK 100 THE RCSB ID CODE IS RCSB009246. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL 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 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 GLY A 3 N SER A 5 1.69 REMARK 500 O GLY B 3 N SER B 5 1.69 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 LYS A 2 -2.99 -46.53 REMARK 500 MET A 4 35.00 6.62 REMARK 500 SER A 5 60.33 -62.65 REMARK 500 LYS A 6 -87.60 -157.37 REMARK 500 MET A 7 89.47 -35.60 REMARK 500 GLN A 9 9.55 -68.84 REMARK 500 VAL A 18 -73.31 -74.17 REMARK 500 LEU A 19 -60.12 -24.48 REMARK 500 LYS B 2 -2.86 -46.69 REMARK 500 MET B 4 35.24 6.65 REMARK 500 SER B 5 60.33 -62.97 REMARK 500 LYS B 6 -87.64 -157.29 REMARK 500 MET B 7 89.44 -35.48 REMARK 500 GLN B 9 9.67 -69.05 REMARK 500 VAL B 18 -73.32 -74.21 REMARK 500 LEU B 19 -60.04 -24.47 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 ARG A 13 0.32 SIDE_CHAIN REMARK 500 ARG A 16 0.15 SIDE_CHAIN REMARK 500 ARG A 23 0.29 SIDE_CHAIN REMARK 500 ARG A 31 0.19 SIDE_CHAIN REMARK 500 ARG A 50 0.12 SIDE_CHAIN REMARK 500 ARG B 13 0.32 SIDE_CHAIN REMARK 500 ARG B 16 0.15 SIDE_CHAIN REMARK 500 ARG B 23 0.29 SIDE_CHAIN REMARK 500 ARG B 31 0.19 SIDE_CHAIN REMARK 500 ARG B 50 0.12 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ARR RELATED DB: PDB REMARK 900 THE MINIMIZED AVERAGE SOLUTION STRUCTURE OF WILD-TYPE ARC REMARK 900 REPRESSOR REMARK 900 RELATED ID: 1PAR RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF WILD-TYPE ARC BOUND TO OPERATOR DNA DBREF 1QTG A 1 53 UNP P03050 RARC_BPP22 1 53 DBREF 1QTG B 1 53 UNP P03050 RARC_BPP22 1 53 SEQADV 1QTG LEU A 11 UNP P03050 ASN SEQADV 1QTG ASN A 12 UNP P03050 LEU SEQADV 1QTG LEU B 11 UNP P03050 ASN SEQADV 1QTG ASN B 12 UNP P03050 LEU SEQRES 1 A 53 MET LYS GLY MET SER LYS MET PRO GLN PHE LEU ASN ARG SEQRES 2 A 53 TRP PRO ARG GLU VAL LEU ASP LEU VAL ARG LYS VAL ALA SEQRES 3 A 53 GLU GLU ASN GLY ARG SER VAL ASN SER GLU ILE TYR GLN SEQRES 4 A 53 ARG VAL MET GLU SER PHE LYS LYS GLU GLY ARG ILE GLY SEQRES 5 A 53 ALA SEQRES 1 B 53 MET LYS GLY MET SER LYS MET PRO GLN PHE LEU ASN ARG SEQRES 2 B 53 TRP PRO ARG GLU VAL LEU ASP LEU VAL ARG LYS VAL ALA SEQRES 3 B 53 GLU GLU ASN GLY ARG SER VAL ASN SER GLU ILE TYR GLN SEQRES 4 B 53 ARG VAL MET GLU SER PHE LYS LYS GLU GLY ARG ILE GLY SEQRES 5 B 53 ALA HELIX 1 1 PHE A 10 TRP A 14 5 5 HELIX 2 2 PRO A 15 GLY A 30 1 16 HELIX 3 3 SER A 32 GLY A 49 1 18 HELIX 4 4 PHE B 10 TRP B 14 5 5 HELIX 5 5 PRO B 15 GLY B 30 1 16 HELIX 6 6 SER B 32 GLY B 49 1 18 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 MASTER 151 0 0 6 0 0 0 6 0 0 0 10 END