1SGT = PDB ID code
HEADER HYDROLASE (SERINE PROTEINASE) 13-APR-88 1SGT 1SGT 3 COMPND TRYPSIN (/SGT$) (E.C.3.4.21.4) 1SGT 4 SOURCE (STREPTOMYCES $GRISEUS, STRAIN K1) 1SGT 5 AUTHOR R.J.READ,M.N.G.JAMES 1SGT 6 REVDAT 1 16-JUL-88 1SGT 0 1SGT 7 JRNL AUTH R.J.READ,M.N.G.JAMES 1SGT 8 JRNL TITL REFINED CRYSTAL STRUCTURE OF STREPTOMYCES $GRISEUS 1SGT 9 JRNL TITL 2 TRYPSIN AT 1.7 ANGSTROMS RESOLUTION 1SGT 10 JRNL REF J.MOL.BIOL. V. 200 523 1988 1SGT 11 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 070 1SGT 12 REMARK 1 1SGT 13 REMARK 1 REFERENCE 1 1SGT 14 REMARK 1 AUTH R.J.READ,G.D.BRAYER,L.JURASEK,M.N.G.JAMES 1SGT 15 REMARK 1 TITL CRITICAL COMPARISON OF COMPARATIVE MODEL BUILDING 1SGT 16 REMARK 1 TITL 2 OF STREPTOMYCES $GRISEUS TRYPSIN 1SGT 17 REMARK 1 REF BIOCHEMISTRY V. 23 6570 1984 1SGT 18 REMARK 1 REFN ASTM BICHAW US ISSN 0006-2960 033 1SGT 19 REMARK 2 1SGT 20 Resolution - Very Important Resolutions < 3A can show side chains accurately Resolutions > 3A often do not show side chains REMARK 2 RESOLUTION. 1.7 ANGSTROMS. 1SGT 21 REMARK 3 1SGT 22 The "R" factor - indicates accuracy of the structure. For a high resolution 1.6A structure, the "R" value should not be higher than .16 REMARK 3 REFINEMENT. BY THE RESTRAINED LEAST SQUARES PROCEDURE OF J. 1SGT 23 REMARK 3 KONNERT AND W. HENDRICKSON (PROGRAM *PROLSQ*). THE R 1SGT 24 REMARK 3 VALUE IS 0.161 FOR 20046 REFLECTIONS IN THE RESOLUTION 1SGT 25 REMARK 3 RANGE 8.0 TO 1.7 ANGSTROMS WITH I .GT. SIGMA(I), WHICH 1SGT 26 REMARK 3 CORRESPONDS TO 80.6 PER CENT OF ALL DATA IN THE RESOLUTION 1SGT 27 REMARK 3 RANGE FROM INFINITY TO 1.7 ANGSTROMS. THE R VALUE IS 1SGT 28 REMARK 3 0.230 FOR ALL DATA (WITH ABS(FOBS) SET TO 0.0 FOR 1SGT 29 REMARK 3 REFLECTIONS WITH NEGATIVE NET INTENSITIES). THE OVERALL 1SGT 30 REMARK 3 RMS ERROR IS 0.24 ANGSTROMS, ESTIMATED BY MEANS OF A 1SGT 31 REMARK 3 SIGMA(SUB)A PLOT (R.J.READ, ACTA CRYSTALLOGR., V. A42, P. 1SGT 32 REMARK 3 140, 1986). 1SGT 33 REMARK 3 1SGT 34 REMARK 3 NUMBER OF PROTEIN ATOMS (INCLUDING CA++) 1621 1SGT 35 REMARK 3 NUMBER OF SOLVENT ATOMS 192 1SGT 36 REMARK 3 NUMBER OF VARIABLE PARAMETERS (POSITIONAL 7442 1SGT 37 REMARK 3 PARAMETERS FOR THE SOLVENT MOLECULE HOH 1SGT 38 REMARK 3 18, WHICH LIES ON A CRYSTALLOGRAPHIC 1SGT 39 REMARK 3 TWO-FOLD AXIS, WERE NOT VARIED) 1SGT 40 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES (THE VALUES OF 1SGT 41 REMARK 3 SIGMA, IN PARENTHESES, ARE THE INPUT ESTIMATED 1SGT 42 REMARK 3 STANDARD DEVIATIONS THAT DETERMINE THE RELATIVE 1SGT 43 REMARK 3 WEIGHTS OF THE CORRESPONDING RESTRAINTS) 1SGT 44 REMARK 3 DISTANCE RESTRAINTS (ANGSTROMS) 1SGT 45 REMARK 3 BOND DISTANCE 0.019(0.014) 1SGT 46 REMARK 3 ANGLE DISTANCE 0.038(0.027) 1SGT 47 REMARK 3 PLANAR 1-4 DISTANCE 0.041(0.027) 1SGT 48 REMARK 3 PLANE RESTRAINT (ANGSTROMS) 0.017(0.016) 1SGT 49 REMARK 3 CHIRAL-CENTER RESTRAINT (ANGSTROMS**3) 0.208(0.130) 1SGT 50 REMARK 3 NON-BONDED CONTACT RESTRAINTS (ANGSTROMS) 1SGT 51 REMARK 3 SINGLE TORSION CONTACT 0.279(0.350) 1SGT 52 REMARK 3 MULTIPLE TORSION CONTACT 0.130(0.350) 1SGT 53 REMARK 3 POSSIBLE HYDROGEN BOND 0.177(0.350) 1SGT 54 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINT (DEGREES) 1SGT 55 REMARK 3 PLANAR (OMEGA) 3.1(2.5) 1SGT 56 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS (ANGSTROMS**2) 1SGT 57 REMARK 3 MAIN-CHAIN BOND 1.816(1.500) 1SGT 58 REMARK 3 MAIN-CHAIN ANGLE 2.535(2.000) 1SGT 59 REMARK 3 SIDE-CHAIN BOND 5.729(3.500) 1SGT 60 REMARK 3 SIDE-CHAIN ANGLE 8.466(5.000) 1SGT 61 REMARK 4 1SGT 62 REMARK 4 THE SEQUENCE NUMBERING IS BASED ON THE SEQUENCE ALIGNMENT 1SGT 63 REMARK 4 WITH CHYMOTRYPSIN. SEE THE REFERENCE CITED IN THE *JRNL* 1SGT 64 REMARK 4 RECORDS ABOVE. THE AMINO ACID SEQUENCE AS DETERMINED BY 1SGT 65 REMARK 4 R.W.OLAFSON,L.JURASEK,M.R.CARPENTER,L.B.SMILLIE 1SGT 66 REMARK 4 (BIOCHEMISTRY, V. 14, P. 1168, 1975) HAS BEEN CORRECTED BY 1SGT 67 REMARK 4 THE INSERTION OF TWO RESIDUES AFTER SER 76. THESE TWO 1SGT 68 REMARK 4 RESIDUES ARE CURRENTLY INTERPRETED FROM THE ELECTRON 1SGT 69 REMARK 4 DENSITY AS GLY-ALA AND ARE NUMBERED 77 AND 79, 1SGT 70 REMARK 4 RESPECTIVELY. 1SGT 71 REMARK 5 1SGT 72 REMARK 5 SGT IS PURIFIED FROM PRONASE, A COMMERCIAL PRODUCT OBTAINED 1SGT 73 REMARK 5 FROM THE EXTRACELLULAR CULTURE FILTRATE OF THE SOIL 1SGT 74 REMARK 5 BACTERIUM STREPTOMYCES GRISEUS, STRAIN K1. 1SGT 75 REMARK 6 1SGT 76 REMARK 6 A NUMBER OF RESIDUES HAVE POOR ELECTRON DENSITY IN THE 1SGT 77 REMARK 6 FINAL MAP. SEE THE *FTNOTE* RECORDS BELOW FOR SPECIFIC 1SGT 78 REMARK 6 DETAILS. 1SGT 79 REMARK 7 1SGT 80 REMARK 7 SITE *CAT* COMPRISES THOSE RESIDUES FORMING THE CATALYTIC 1SGT 81 REMARK 7 SITE. 1SGT 82 REMARK 8 1SGT 83 REMARK 8 SHEETS S1 AND S2 ARE BOTH SIX-STRANDED SHEETS FORMING A 1SGT 84 REMARK 8 BETA-BARREL. THIS IS REPRESENTED ON THE SHEET RECORDS 1SGT 85 REMARK 8 BELOW BY A SEVEN-STRANDED SHEET WITH THE FIRST AND LAST 1SGT 86 REMARK 8 STRANDS IDENTICAL. 1SGT 87 REMARK 9 1SGT 88 REMARK 9 THE WATERS ARE NUMBERED IN INCREASING ORDER OF ESTIMATED 1SGT 89 REMARK 9 POSITIONAL STANDARD DEVIATION, SO THAT THE WATERS WITH THE 1SGT 90 REMARK 9 LOWEST SEQUENCE NUMBERS SHOULD BE THE MOST RELIABLE. 1SGT 91 SEQRES 1 223 VAL VAL GLY GLY THR ARG ALA ALA GLN GLY GLU PHE PRO 1SGT 92 SEQRES 2 223 PHE MET VAL ARG LEU SER MET GLY CYS GLY GLY ALA LEU 1SGT 93 SEQRES 3 223 TYR ALA GLN ASP ILE VAL LEU THR ALA ALA HIS CYS VAL 1SGT 94 SEQRES 4 223 SER GLY SER GLY ASN ASN THR SER ILE THR ALA THR GLY 1SGT 95 SEQRES 5 223 GLY VAL VAL ASP LEU GLN SER GLY ALA ALA VAL LYS VAL 1SGT 96 SEQRES 6 223 ARG SER THR LYS VAL LEU GLN ALA PRO GLY TYR ASN GLY 1SGT 97 SEQRES 7 223 THR GLY LYS ASP TRP ALA LEU ILE LYS LEU ALA GLN PRO 1SGT 98 SEQRES 8 223 ILE ASN GLN PRO THR LEU LYS ILE ALA THR THR THR ALA 1SGT 99 SEQRES 9 223 TYR ASN GLN GLY THR PHE THR VAL ALA GLY TRP GLY ALA 1SGT 100 SEQRES 10 223 ASN ARG GLU GLY GLY SER GLN GLN ARG TYR LEU LEU LYS 1SGT 101 SEQRES 11 223 ALA ASN VAL PRO PHE VAL SER ASP ALA ALA CYS ARG SER 1SGT 102 SEQRES 12 223 ALA TYR GLY ASN GLU LEU VAL ALA ASN GLU GLU ILE CYS 1SGT 103 SEQRES 13 223 ALA GLY TYR PRO ASP THR GLY GLY VAL ASP THR CYS GLN 1SGT 104 SEQRES 14 223 GLY ASP SER GLY GLY PRO MET PHE ARG LYS ASP ASN ALA 1SGT 105 SEQRES 15 223 ASP GLU TRP ILE GLN VAL GLY ILE VAL SER TRP GLY TYR 1SGT 106 SEQRES 16 223 GLY CYS ALA ARG PRO GLY TYR PRO GLY VAL TYR THR GLU 1SGT 107 SEQRES 17 223 VAL SER THR PHE ALA SER ALA ILE ALA SER ALA ALA ARG 1SGT 108 SEQRES 18 223 THR LEU 1SGT 109 FTNOTE 1 1SGT 110 NOTE - Not all atoms show up well. Some parts of the chain may be missing in the final structure. A single protein may appear as multiple chains because the connecting loops do not difract well and thus will not give a good structure. FTNOTE 1 THR 20 - POSSIBLE STATIC DISORDER WITH CHI 1 ROTATED BY 1SGT 111 FTNOTE 1 -120 DEGREES. 1SGT 112 FTNOTE 2 1SGT 113 FTNOTE 2 ARG 21 - POOR DENSITY FOR GUANIDINIUM GROUP. 1SGT 114 FTNOTE 3 1SGT 115 FTNOTE 3 THR 65 - POSSIBLE STATIC DISORDER WITH CHI 1 ROTATED BY 1SGT 116 FTNOTE 3 +120 DEGREES. 1SGT 117 FTNOTE 4 1SGT 118 FTNOTE 4 LYS 82 - GOOD DENSITY UP TO NZ WHICH IS NOT VISIBLE. 1SGT 119 FTNOTE 5 1SGT 120 FTNOTE 5 ARG 84 - NOISY DENSITY BEYOND CD. 1SGT 121 FTNOTE 6 1SGT 122 FTNOTE 6 LYS 87 - VERY WEAK DENSITY BEYOND CD. 1SGT 123 FTNOTE 7 1SGT 124 FTNOTE 7 THR 98 - POSSIBLE STATIC DISORDER WITH CHI 1 ROTATED BY 1SGT 125 FTNOTE 7 +120 DEGREES. 1SGT 126 FTNOTE 8 1SGT 127 FTNOTE 8 GLN 110 - NOISY SIDE CHAIN DENSITY. 1SGT 128 FTNOTE 9 1SGT 129 FTNOTE 9 LYS 122 - WEAK DENSITY BEYOND CG. 1SGT 130 FTNOTE 10 1SGT 131 FTNOTE 10 GLN 133 - CHI 3 ANGLE DIFFICULT TO ESTABLISH FROM DENSITY. 1SGT 132 FTNOTE 11 1SGT 133 FTNOTE 11 ARG 145 - NOISY AND AMBIGUOUS SIDE CHAIN DENSITY, 1SGT 134 FTNOTE 11 PROJECTING INTO SOLVENT. 1SGT 135 FTNOTE 12 1SGT 136 FTNOTE 12 ASN 174 - LITTLE DENSITY FOR OD1 AND ND2. 1SGT 137 FTNOTE 13 1SGT 138 FTNOTE 13 GLN 192 - DENSITY NOISY AND WEAK BEYOND CB. 1SGT 139 FTNOTE 14 1SGT 140 FTNOTE 14 ASN 204 - NOISY DENSITY, POSSIBLY DUE TO STATIC DISORDER 1SGT 141 FTNOTE 14 AROUND CHI 1. 1SGT 142 FTNOTE 15 1SGT 143 FTNOTE 15 ASP 205 - VERY WEAK DENSITY FOR CB, NOISY DENSITY FOR 1SGT 144 FTNOTE 15 CARBOXYL GROUP. 1SGT 145 FTNOTE 16 1SGT 146 FTNOTE 16 SER 236 - POSSIBLE STATIC DISORDER ABOUT CHI 1. 1SGT 147 FTNOTE 17 1SGT 148 FTNOTE 17 ARG 243 - VERY NOISY DENSITY, SIDE CHAIN PAST CG IS 1SGT 149 FTNOTE 17 ESSENTIALLY ARBITRARY. 1SGT 150 IMPORTANT INFO - Heteroatoms, including water HET CA 246 1 CALCIUM ++ ION 1SGT 151 FORMUL 2 CA CA1 ++ 1SGT 152 FORMUL 3 HOH *192(H2 O1) 1SGT 153 Structural Info - The location of the helices and the sheets is determined by the crystallographer. Not by the modeling software. If this info is not in the PDB file, the modeling software will not know where to draw the ribbons in a ribbon diagram. HELIX 1 A ALA 56 CYS 58 5 1SGT 154 HELIX 2 B1 ASP 165 TYR 172 1 1SGT 155 HELIX 3 B2 GLY 173 GLU 175 5 1SGT 156 HELIX 4 C1 VAL 231 ARG 243 1 1SGT 157 HELIX 5 C2 ALA 242 THR 244 5 1SGT 158 SHEET 1 S1 7 MET 30 LEU 33 0 1SGT 159 SHEET 2 S1 7 CYS 42 ALA 48 -1 O GLY 44 N VAL 31 1SGT 160 SHEET 3 S1 7 ILE 51 THR 54 -1 O LEU 53 N ALA 45 1SGT 161 SHEET 4 S1 7 ALA 104 LEU 108 -1 O ILE 106 N VAL 52 1SGT 162 SHEET 5 S1 7 VAL 81 GLN 90 -1 O LEU 89 N LEU 105 1SGT 163 SHEET 6 S1 7 THR 65 GLY 68 -1 O GLY 68 N VAL 81 1SGT 164 SHEET 7 S1 7 MET 30 LEU 33 -1 O ARG 32 N THR 67 1SGT 165 SHEET 1 S2 7 THR 135 GLY 140 0 1SGT 166 SHEET 2 S2 7 LEU 156 VAL 163 -1 O VAL 160 N PHE 136 1SGT 167 SHEET 3 S2 7 GLU 180 ALA 183 -1 O CYS 182 N VAL 163 1SGT 168 SHEET 4 S2 7 GLY 226 GLU 230 -1 O TYR 228 N ILE 181 1SGT 169 SHEET 5 S2 7 TRP 207 TRP 215 -1 O TRP 215 N VAL 227 1SGT 170 SHEET 6 S2 7 PRO 198 LYS 202 -1 O ARG 201 N ILE 208 1SGT 171 SHEET 7 S2 7 THR 135 GLY 140 -1 O THR 137 N PHE 200 1SGT 172 TURN 1 T1 ALA 23 GLU 26 1SGT 173 TURN 2 T2 PHE 27 MET 30 1SGT 174 TURN 3 T3 LEU 33 GLY 41 1SGT 175 TURN 4 T4 ALA 48 ILE 51 1SGT 176 TURN 5 T5 ASP 72 SER 76 1SGT 177 TURN 6 T6 SER 76 ALA 80 1SGT 178 TURN 7 T7 ALA 91 TYR 94 1SGT 179 TURN 8 T8 THR 129 ASN 132 1SGT 180 TURN 9 T9 ARG 145 GLY 149 1SGT 181 TURN 10 T10 CYS 168 ALA 171 1SGT 182 TURN 11 T11 VAL 177 GLU 179 1SGT 183 TURN 12 T12 CYS 191 ASP 194 1SGT 184 TURN 13 T13 ASP 194 GLY 197 1SGT 185 TURN 14 T14 ASP 203 ASP 205 1SGT 186 TURN 15 T15 ARG 222 TYR 224 1SGT 187 SSBOND 1 CYS 42 CYS 58 1SGT 188 SSBOND 2 CYS 168 CYS 182 1SGT 189 SSBOND 3 CYS 191 CYS 220 1SGT 190 SITE 1 CAT 3 HIS 57 ASP 102 SER 195 1SGT 191 CRYST1 72.290 50.980 120.090 90.00 90.00 90.00 C 2 2 21 8 1SGT 192 ORIGX1 1.000000 0.000000 0.000000 0.00000 1SGT 193 ORIGX2 0.000000 1.000000 0.000000 0.00000 1SGT 194 ORIGX3 0.000000 0.000000 1.000000 0.00000 1SGT 195 SCALE1 0.013833 0.000000 0.000000 0.00000 1SGT 196 SCALE2 0.000000 0.019616 0.000000 0.00000 1SGT 197 SCALE3 0.000000 0.000000 0.008327 0.00000 1SGT 198