HEADER GENE REGULATION 27-JUN-99 1QTG TITLE AVERAGED NMR MODEL OF SWITCH ARC, A DOUBLE MUTANT OF ARC REPRESSOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REPRESSOR ARC; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEDERBERGVIRUS P22; SOURCE 3 ORGANISM_TAXID: 10754; SOURCE 4 GENE: ARC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET800-SWITCH_ARC; SOURCE 9 OTHER_DETAILS: MUTATED SYNTHETIC ARC GENE KEYWDS BETA-SHEET, RIGHT-HANDED HELIX, STRUCTURAL CHANGE, GENE REGULATION EXPDTA SOLUTION NMR AUTHOR M.H.J.CORDES,N.P.WALSH,C.J.MCKNIGHT,R.T.SAUER REVDAT 5 21-DEC-22 1QTG 1 COMPND SOURCE DBREF SEQADV REVDAT 4 02-MAR-22 1QTG 1 REMARK 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 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: REMARK 3 GENERATION OF THIS MODEL OF THE SWITCH ARC MUTANT INVOLVED A REMARK 3 COMBINATION OF EXPERIMENTAL AND SIMU REMARK 3 LATED DISTANCE RESTRAINTS. FOR RESIDUES 7-14, 81 NOE CROSSPEAKS REMARK 3 WERE OBTAINED FROM A 50-MS 2D NOES REMARK 3 Y SPECTRUM AND WERE TRANSLATED INTO STRONG (1.8-2.8 A), MEDIUM REMARK 3 (1.8-3.3 A), MEDIUM-WEAK (1.8-3.8 A REMARK 3 ) AND WEAK (1.8-4.3 A) DISTANCE RESTRAINTS.18 ADDITIONAL REMARK 3 CROSSPEAKS WERE OBTAINED FROM A 150-MS 3D REMARK 3 NOESY SPECTRUM AND WERE ASSIGNED LOOSER RESTRAINTS (1.8 TO 4.0 A REMARK 3 OR 1.8 TO 6.0 A)BECAUSE OF THE L REMARK 3 ONGER MIXING TIME USED IN THIS EXPERIMENT. TO SIMULATE THE REMARK 3 STRUCTURE OF RESIDUES 14 TO 53 (RESIDUE REMARK 3 14 WAS DESCRIBED BY BOTH ACTUAL AND COMPUTED RESTRAINTS), A LIST REMARK 3 OF 1635 DISTANCES WAS GENERATED REMARK 3 BETWEEN PAIRS OF HEAVY ATOMS WITHIN 4 A OF EACH OTHER IN THE WILD- REMARK 3 TYPE ARC CRYSTAL STRUCTURE, AND REMARK 3 THE INTERATOMIC DISTANCES WERE CONSTRAINED TO BE WITHIN + OR - 1.0 REMARK 3 A OF THIS VALUE. 28 INITIAL STR REMARK 3 UCTURES WITH RANDOM CONFIGURATIONS FOR RESIDUES 1 TO 13 WERE REMARK 3 GENERATED BY PERFORMING A SET OF CALC REMARK 3 ULATIONS WITH ONLY THE SIMULATED RESTRAINTS FOR RESIDUES 14 TO 53. REMARK 3 THEN, 28 MODEL STRUCTURES WERE REMARK 3 GENERATED BY INCLUDING THE EXPERIMENTAL RESTRAINTS FOR RESIDUES 7 REMARK 3 TO 14. NO RESTRAINTS WERE USED F REMARK 3 OR RESIDUES 1 TO 6, WHICH APPEAR TO BE DISORDERED. AMBIGUITIES IN REMARK 3 INTRA- AND INTERMOLECULAR NOE AS REMARK 3 SIGNMENT RESULTING FROM ARC'S TWOFOLD SYMMETRY WERE RESOLVED REMARK 3 COMPUTATIONALLY AS DESCRIBED (M. NILG REMARK 3 ES, PROTEIN STRUCT. FUNCT. GENET. 17, 297 (1993).19 OF 28 REMARK 3 STRUCTURES WERE ACCEPTED WITH NO NOE VIO REMARK 3 LATIONS GREATER THAN 0.3 A. THE FIVE STRUCTURES WITH THE HIGHEST REMARK 3 ENERGY, WHICH ALSO CONTAINED BACK REMARK 3 BONE DIHEDRAL ANGLES IN DISALLOWED REGIONS OF RAMACHANDRAN SPACE, REMARK 3 WERE DISCARDED. THE REMAINING 14 REMARK 3 STRUCTURES, WHICH HAD PAIRWISE RMSD'S OF 0.6 A (BACKBONE) AND 1.6 REMARK 3 A (HEAVY), WERE USED TO GENERAT REMARK 3 E A MINIMIZED AVERAGE MODEL. REMARK 4 REMARK 4 1QTG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUN-99. REMARK 100 THE DEPOSITION ID IS D_1000009246. 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 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 HA MET B 1 HB3 SER B 5 1.26 REMARK 500 HA MET A 1 HB3 SER A 5 1.26 REMARK 500 HH11 ARG A 50 HG23 VAL B 25 1.26 REMARK 500 HG23 VAL A 25 HH11 ARG B 50 1.27 REMARK 500 H SER A 5 HZ1 LYS A 6 1.28 REMARK 500 HG3 MET B 1 H LYS B 2 1.28 REMARK 500 HG3 MET A 1 H LYS A 2 1.29 REMARK 500 O LEU B 11 H TRP B 14 1.39 REMARK 500 O LEU A 11 H TRP A 14 1.39 REMARK 500 O MET A 4 H LYS A 6 1.47 REMARK 500 O MET B 4 H LYS B 6 1.47 REMARK 500 O GLY A 3 H SER A 5 1.52 REMARK 500 O GLY B 3 H SER B 5 1.52 REMARK 500 N SER B 5 HZ2 LYS B 6 1.53 REMARK 500 O VAL B 18 H LEU B 21 1.59 REMARK 500 O VAL A 18 H LEU A 21 1.59 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 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 11 ENGINEERED MUTATION SEQADV 1QTG ASN A 12 UNP P03050 LEU 12 ENGINEERED MUTATION SEQADV 1QTG LEU B 11 UNP P03050 ASN 11 ENGINEERED MUTATION SEQADV 1QTG ASN B 12 UNP P03050 LEU 12 ENGINEERED MUTATION 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