HEADER GENE-REGULATING PROTEIN 22-MAR-94 1PAR 1PAR 2 COMPND ARC REPRESSOR AND A SYNTHETIC 22-MER DNA (21 BASE-PAIRS AND 1PAR 3 COMPND 2 ONE BASE 5' OVERHANG) CONTAINING THE SEQUENCE OF THE ARC 1PAR 4 COMPND 3 OPERATOR 1PAR 5 SOURCE BACTERIOPHAGE P22 1PAR 6 AUTHOR B.E.RAUMANN,M.A.ROULD,C.O.PABO,R.T.SAUER 1PAR 7 REVDAT 1 31-JUL-94 1PAR 0 1PAR 8 REMARK 1 1PAR 9 REMARK 1 REFERENCE 1 1PAR 10 REMARK 1 AUTH B.E.RAUMANN,M.A.ROULD,C.O.PABO,R.T.SAUER 1PAR 11 REMARK 1 TITL DNA RECOGNITION BY BETA-SHEETS IN THE ARC 1PAR 12 REMARK 1 TITL 2 REPRESSOR-OPERATOR CRYSTAL STRUCTURE 1PAR 13 REMARK 1 REF PLANT MOL.BIOL. V. 367 754 1994 1PAR 14 REMARK 1 REFN ASTM PMBIDB NE ISSN 0167-4412 2006 1PAR 15 REMARK 2 1PAR 16 REMARK 2 RESOLUTION. 2.6 ANGSTROMS. 1PAR 17 REMARK 3 1PAR 18 REMARK 3 REFINEMENT. 1PAR 19 REMARK 3 PROGRAM 1 X-PLOR 1PAR 20 REMARK 3 AUTHORS 1 BRUNGER 1PAR 21 REMARK 3 PROGRAM 2 TNT 1PAR 22 REMARK 3 AUTHORS 2 TRONRUD,TEN EYCK,MATTHEWS 1PAR 23 REMARK 3 R VALUE 0.225 1PAR 24 REMARK 3 RMSD BOND DISTANCES 0.010 ANGSTROMS 1PAR 25 REMARK 3 RMSD BOND ANGLES 1.51 DEGREES 1PAR 26 REMARK 3 1PAR 27 REMARK 3 NUMBER OF REFLECTIONS 11253 1PAR 28 REMARK 3 RESOLUTION RANGE 21.0 - 2.6 ANGSTROMS 1PAR 29 REMARK 3 DATA CUTOFF 0.0 SIGMA(F) 1PAR 30 REMARK 3 PERCENT COMPLETION 95.0 1PAR 31 REMARK 3 1PAR 32 REMARK 3 NUMBER OF PROTEIN ATOMS 1712 1PAR 33 REMARK 3 NUMBER OF NUCLEIC ACID ATOMS 896 1PAR 34 REMARK 3 NUMBER OF SOLVENT ATOMS 45 1PAR 35 REMARK 3 1PAR 36 REMARK 3 HEAVY ATOM DERIVATIVE DATA WERE COLLECTED FROM A CRYSTAL 1PAR 37 REMARK 3 CONTAINING 5-IODO-URIDINE AT OPERATOR POSITIONS 3 AND 103. 1PAR 38 REMARK 3 SINGLE ISOMORPHOUS REPLACEMENT/ANOMALOUS SCATTERING PHASES 1PAR 39 REMARK 3 WERE CALCULATED WITH PHARE OF THE CCP4 SUITE OF PROGRAMS 1PAR 40 REMARK 3 (1). FRODO (2) WAS USE D FOR MODEL BUILDING AN D RIGID 1PAR 41 REMARK 3 BODY MINIMIZATION, POWELL POSITIONAL MINIMIZATION, AND 1PAR 42 REMARK 3 SIMULATED ANNEALING REFINEMENT WERE DONE WITH X-PLOR (3). 1PAR 43 REMARK 3 THE MODEL WAS CHECKED AND REBUILT USING SIMULATED 1PAR 44 REMARK 3 ANNEALING OMIT MAP. AT THE LAST STAGE OF REFINEMENT, 1PAR 45 REMARK 3 TIGHTLY RESTRAINED INDIVIDUAL B-FACTORS AND 45 WATER 1PAR 46 REMARK 3 MOLECULES WERE INCLUDED, AND CONVENTIONAL LEAST SQUARES 1PAR 47 REMARK 3 REFINEMENT WITH TNT (4) WAS USED. (1) S.E.R.C. (U.K.) 1PAR 48 REMARK 3 COLLABORATIVE COMPUTING PROJECT NO. 4 (DARESBURY 1PAR 49 REMARK 3 LABORATORY, WARRINGTON, U.K., 1979). (2) JONES, T. A 1PAR 50 REMARK 3 J.APPL.CRYSTALLOGR. 11, 268-272 (1978). (3) BRUNGER, A.T. 1PAR 51 REMARK 3 X-PLOR V3.1 MANUAL (YALE UNIVERSITY PRESS, NEW HAVEN, 1PAR 52 REMARK 3 1992). (4) TRONRUD, D.E., TEN EYCK, L.F. AND MATTHEWS, 1PAR 53 REMARK 3 B.W. ACTA CRYSTALLOGR. 43, 489-501 (1987). 1PAR 54 REMARK 4 1PAR 55 REMARK 4 THE SITE PRESENTED IN *SITE* RECORDS BELOW IS THE WILD-TYPE 1PAR 56 REMARK 4 SEQUENCE OF THE ARC OPERATOR SITE. 1PAR 57 REMARK 5 1PAR 58 REMARK 5 THE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW 1PAR 59 REMARK 5 WILL YIELD APPROXIMATE COORDINATES FOR CHAIN A WHEN APPLIED 1PAR 60 REMARK 5 TO CHAIN B (DIMER SYMMETRY AXIS). THE TRANSFORMATION 1PAR 61 REMARK 5 PRESENTED ON *MTRIX 2* RECORDS BELOW WILL YIELD APPROXIMATE 1PAR 62 REMARK 5 COORDINATES FOR CHAIN C WHEN APPLIED TO CHAIN D (DIMER 1PAR 63 REMARK 5 SYMMETRY AXIS). THE TRANSFORMATION PRESENTED ON *MTRIX 3* 1PAR 64 REMARK 5 RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS 1PAR 65 REMARK 5 A AND B WHEN APPLIED TO CHAINS C AND D, RESPECTIVELY. THIS 1PAR 66 REMARK 5 THIRD TRANSFORMATION RELATES DIMER CD AND THE RIGHT 1PAR 67 REMARK 5 OPERATOR HALF-SITE TO DIMER AB AND THE LEFT OPERATOR 1PAR 68 REMARK 5 HALF-SITE. (TETRAMER SYMMETRY AXIS). 1PAR 69 REMARK 6 1PAR 70 REMARK 6 RESIDUES ALA A 53 AND ILE C 51 - ALA C 53 ARE NOT INCLUDED 1PAR 71 REMARK 6 IN THE MODEL DUE TO POOR ELECTRON DENSITY. 1PAR 72 REMARK 7 1PAR 73 REMARK 7 THE SIDE CHAIN IS INCOMPLETE FOR RESIDUE GLU C 48. 1PAR 74 REMARK 8 1PAR 75 REMARK 8 BY REQUEST OF THE DEPOSITOR, THE PROTEIN DATA BANK HAS NOT 1PAR 76 REMARK 8 APPLIED THE IUPAC-IUB RECOMMENDATIONS REGARDING THE 1PAR 77 REMARK 8 DESIGNATION OF BRANCHES 1 AND 2 OF SIDE-CHAIN ATOMS IN 1PAR 78 REMARK 8 RESIDUES ARG, ASP, GLU, LEU, PHE, TYR, AND VAL TO THIS 1PAR 79 REMARK 8 ENTRY. 1PAR 80 REMARK 9 1PAR 81 REMARK 9 PDB ADVISORY NOTICE: 1PAR 82 REMARK 9 WATER MOLECULE 636 MAKES A CLOSE CONTACT OF 2.O8 ANGSTROMS 1PAR 83 REMARK 9 WITH ATOM N7 OF RESIDUE A 2 OF CHAIN *E*. 1PAR 84 SEQRES 1 A 53 MET LYS GLY MET SER LYS MET PRO GLN PHE ASN LEU ARG 1PAR 85 SEQRES 2 A 53 TRP PRO ARG GLU VAL LEU ASP LEU VAL ARG LYS VAL ALA 1PAR 86 SEQRES 3 A 53 GLU GLU ASN GLY ARG SER VAL ASN SER GLU ILE TYR GLN 1PAR 87 SEQRES 4 A 53 ARG VAL MET GLU SER PHE LYS LYS GLU GLY ARG ILE GLY 1PAR 88 SEQRES 5 A 53 ALA 1PAR 89 SEQRES 1 B 53 MET LYS GLY MET SER LYS MET PRO GLN PHE ASN LEU ARG 1PAR 90 SEQRES 2 B 53 TRP PRO ARG GLU VAL LEU ASP LEU VAL ARG LYS VAL ALA 1PAR 91 SEQRES 3 B 53 GLU GLU ASN GLY ARG SER VAL ASN SER GLU ILE TYR GLN 1PAR 92 SEQRES 4 B 53 ARG VAL MET GLU SER PHE LYS LYS GLU GLY ARG ILE GLY 1PAR 93 SEQRES 5 B 53 ALA 1PAR 94 SEQRES 1 C 53 MET LYS GLY MET SER LYS MET PRO GLN PHE ASN LEU ARG 1PAR 95 SEQRES 2 C 53 TRP PRO ARG GLU VAL LEU ASP LEU VAL ARG LYS VAL ALA 1PAR 96 SEQRES 3 C 53 GLU GLU ASN GLY ARG SER VAL ASN SER GLU ILE TYR GLN 1PAR 97 SEQRES 4 C 53 ARG VAL MET GLU SER PHE LYS LYS GLU GLY ARG ILE GLY 1PAR 98 SEQRES 5 C 53 ALA 1PAR 99 SEQRES 1 D 53 MET LYS GLY MET SER LYS MET PRO GLN PHE ASN LEU ARG 1PAR 100 SEQRES 2 D 53 TRP PRO ARG GLU VAL LEU ASP LEU VAL ARG LYS VAL ALA 1PAR 101 SEQRES 3 D 53 GLU GLU ASN GLY ARG SER VAL ASN SER GLU ILE TYR GLN 1PAR 102 SEQRES 4 D 53 ARG VAL MET GLU SER PHE LYS LYS GLU GLY ARG ILE GLY 1PAR 103 SEQRES 5 D 53 ALA 1PAR 104 SEQRES 1 E 22 T A T A G T A G A G T G C 1PAR 105 SEQRES 2 E 22 T T C T A T C A T 1PAR 106 SEQRES 1 F 22 A A T G A T A G A A G C A 1PAR 107 SEQRES 2 F 22 C T C T A C T A T 1PAR 108 FORMUL 8 HOH *45(H2 O1) 1PAR 109 HELIX 1 A PRO A 15 GLY A 30 1 HELIX A IN MONOMER A 1PAR 110 HELIX 2 B SER A 32 GLU A 48 1 HELIX B IN MONOMER A 1PAR 111 HELIX 3 A PRO B 15 GLY B 30 1 HELIX A IN MONOMER B 1PAR 112 HELIX 4 B SER B 32 GLU B 48 1 HELIX B IN MONOMER B 1PAR 113 HELIX 5 A PRO C 15 GLY C 30 1 HELIX A IN MONOMER C 1PAR 114 HELIX 6 B SER C 32 GLU C 48 1 HELIX B IN MONOMER C 1PAR 115 HELIX 7 A PRO D 15 GLY D 30 1 HELIX A IN MONOMER D 1PAR 116 HELIX 8 B SER D 32 GLU D 48 1 HELIX B IN MONOMER D 1PAR 117 SHEET 1 AB 2 PRO A 8 TRP A 14 0 1PAR 118 SHEET 2 AB 2 PRO B 8 TRP B 14 -1 O PHE B 10 N LEU A 12 1PAR 119 SHEET 1 CD 2 PRO C 8 TRP C 14 0 1PAR 120 SHEET 2 CD 2 PRO D 8 TRP D 14 -1 O PHE D 10 N LEU C 12 1PAR 121 TURN 1 A1 MET A 1 MET A 4 TYPE II TURN 1PAR 122 TURN 2 A2 MET A 4 MET A 7 TYPE I TURN 1PAR 123 TURN 3 B1 MET B 1 MET B 4 TYPE II TURN 1PAR 124 TURN 4 B2 MET B 4 MET B 7 TYPE I TURN 1PAR 125 TURN 5 C1 MET C 1 MET C 4 TYPE II TURN 1PAR 126 TURN 6 C2 MET C 4 MET C 7 TYPE I TURN 1PAR 127 TURN 7 D1 MET D 1 MET D 4 TYPE II TURN 1PAR 128 TURN 8 D2 MET D 4 MET D 7 TYPE I TURN 1PAR 129 SITE 1 AOP 4 A E 2 T E 22 A F 2 T F 22 1PAR 130 CRYST1 65.670 56.730 53.800 90.00 106.90 90.00 P 21 8 1PAR 131 ORIGX1 1.000000 0.000000 0.000000 0.00000 1PAR 132 ORIGX2 0.000000 1.000000 0.000000 0.00000 1PAR 133 ORIGX3 0.000000 0.000000 1.000000 0.00000 1PAR 134 SCALE1 0.015228 0.000000 0.004627 0.00000 1PAR 135 SCALE2 0.000000 0.017627 0.000000 0.00000 1PAR 136 SCALE3 0.000000 0.000000 0.019426 0.00000 1PAR 137 MTRIX1 1 -0.511800 0.112700 -0.851700 63.45470 1 1PAR 138 MTRIX2 1 0.130700 -0.969600 -0.206800 -8.03550 1 1PAR 139 MTRIX3 1 -0.849100 -0.217200 0.481500 35.21450 1 1PAR 140 MTRIX1 2 0.535600 0.039500 -0.843500 58.08270 1 1PAR 141 MTRIX2 2 0.042600 -0.998900 -0.019800 -4.33970 1 1PAR 142 MTRIX3 2 -0.843400 -0.025300 -0.536700 105.34710 1 1PAR 143 MTRIX1 3 0.014600 0.119900 -0.992700 70.37200 1 1PAR 144 MTRIX2 3 0.100400 -0.987900 -0.117900 -5.90280 1 1PAR 145 MTRIX3 3 -0.994800 -0.098000 -0.026400 71.22350 1 1PAR 146