0.017492 0.000000 0.000000 0.000000 0.016439 0.000000 0.000000 0.000000 0.030404 0.00000 0.00000 0.00000 Muraki, M. Harata, K. Goda, S. Nagahora, H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 90.00 90.00 57.170 60.830 32.890 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking N O3 -1 62.005 NITRATE ION non-polymer C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking US Protein Sci. PRCIEI 0795 0961-8368 6 473 476 9041653 Importance of van der Waals contact between Glu 35 and Trp 109 to the catalytic action of human lysozyme. 1997 NE Biochim.Biophys.Acta BBACAQ 0113 0006-3002 916 66 The Roles of Conserved Aromatic Amino-Acid Residues in the Active Site of Human Lysozyme: A Site-Specific Mutagenesis Study 1987 10.2210/pdb1jkc/pdb pdb_00001jkc 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 DIFFRACTOMETER ENRAF-NONIUS FAST M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE ENRAF-NONIUS FR571 14681.658 LYSOZYME 3.2.1.17 W109F 1 man polymer 62.005 NITRATE ION 2 syn non-polymer 18.015 water 85 nat water no no KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLS CSALLQDNIADAVACAKRVVRDPQGIRAFVAWRNRCQNRDVRQYVQGCGV KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLS CSALLQDNIADAVACAKRVVRDPQGIRAFVAWRNRCQNRDVRQYVQGCGV A polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n human Homo baker's yeast Saccharomyces sample A SYNTHETIC GENE OF HUMAN LYSO 9606 Homo sapiens A SYNTHETIC GENE OF HUMAN LYSOZYME WITH A MUTATION OF W109F 4932 Saccharomyces cerevisiae KSC22-1C YEP YEPHLYSIG (PHE109) 1.95 37. 4.5 5 M NH4NO3 IN 20 MM NA ACETATE (PH4.5) diffrn_detector pdbx_database_status database_2 struct_ref_seq_dif struct_site pdbx_initial_refinement_model repository Initial release Version format compliance Version format compliance Data collection Other Database references Derived calculations Refinement description 1 0 1997-05-15 1 1 2008-03-03 1 2 2011-07-13 1 3 2018-04-18 1 4 2021-11-03 1 5 2023-08-09 _diffrn_detector.detector _pdbx_database_status.process_site _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Y BNL 1996-11-13 REL REL NO3 NITRATE ION HOH water 1LZ1 PDB ENTRY 1LZ1 PDB experimental model NO3 1 2 NO3 NO3 131 A NO3 2 2 NO3 NO3 132 A HOH 1 3 HOH HOH 133 A HOH 2 3 HOH HOH 134 A HOH 3 3 HOH HOH 135 A HOH 4 3 HOH HOH 136 A HOH 5 3 HOH HOH 137 A HOH 6 3 HOH HOH 138 A HOH 7 3 HOH HOH 139 A HOH 8 3 HOH HOH 140 A HOH 9 3 HOH HOH 141 A HOH 10 3 HOH HOH 142 A HOH 11 3 HOH HOH 143 A HOH 12 3 HOH HOH 144 A HOH 13 3 HOH HOH 145 A HOH 14 3 HOH HOH 146 A HOH 15 3 HOH HOH 147 A HOH 16 3 HOH HOH 148 A HOH 17 3 HOH HOH 149 A HOH 18 3 HOH HOH 150 A HOH 19 3 HOH HOH 151 A HOH 20 3 HOH HOH 152 A HOH 21 3 HOH HOH 153 A HOH 22 3 HOH HOH 154 A HOH 23 3 HOH HOH 155 A HOH 24 3 HOH HOH 156 A HOH 25 3 HOH HOH 157 A HOH 26 3 HOH HOH 158 A HOH 27 3 HOH HOH 159 A HOH 28 3 HOH HOH 160 A HOH 29 3 HOH HOH 161 A HOH 30 3 HOH HOH 162 A HOH 31 3 HOH HOH 163 A HOH 32 3 HOH HOH 164 A HOH 33 3 HOH HOH 165 A HOH 34 3 HOH HOH 166 A HOH 35 3 HOH HOH 167 A HOH 36 3 HOH HOH 168 A HOH 37 3 HOH HOH 169 A HOH 38 3 HOH HOH 170 A HOH 39 3 HOH HOH 171 A HOH 40 3 HOH HOH 172 A HOH 41 3 HOH HOH 173 A HOH 42 3 HOH HOH 174 A HOH 43 3 HOH HOH 175 A HOH 44 3 HOH HOH 176 A HOH 45 3 HOH HOH 177 A HOH 46 3 HOH HOH 178 A HOH 47 3 HOH HOH 179 A HOH 48 3 HOH HOH 180 A HOH 49 3 HOH HOH 181 A HOH 50 3 HOH HOH 182 A HOH 51 3 HOH HOH 183 A HOH 52 3 HOH HOH 184 A HOH 53 3 HOH HOH 185 A HOH 54 3 HOH HOH 186 A HOH 55 3 HOH HOH 187 A HOH 56 3 HOH HOH 188 A HOH 57 3 HOH HOH 189 A HOH 58 3 HOH HOH 190 A HOH 59 3 HOH HOH 191 A HOH 60 3 HOH HOH 192 A HOH 61 3 HOH HOH 193 A HOH 62 3 HOH HOH 194 A HOH 63 3 HOH HOH 195 A HOH 64 3 HOH HOH 196 A HOH 65 3 HOH HOH 197 A HOH 66 3 HOH HOH 198 A HOH 67 3 HOH HOH 199 A HOH 68 3 HOH HOH 200 A HOH 69 3 HOH HOH 201 A HOH 70 3 HOH HOH 202 A HOH 71 3 HOH HOH 203 A HOH 72 3 HOH HOH 204 A HOH 73 3 HOH HOH 205 A HOH 74 3 HOH HOH 206 A HOH 75 3 HOH HOH 207 A HOH 76 3 HOH HOH 208 A HOH 77 3 HOH HOH 209 A HOH 78 3 HOH HOH 210 A HOH 79 3 HOH HOH 211 A HOH 80 3 HOH HOH 212 A HOH 81 3 HOH HOH 213 A HOH 82 3 HOH HOH 214 A HOH 83 3 HOH HOH 215 A HOH 84 3 HOH HOH 216 A HOH 85 3 HOH HOH 217 A LYS 1 n 1 LYS 1 A VAL 2 n 2 VAL 2 A PHE 3 n 3 PHE 3 A GLU 4 n 4 GLU 4 A ARG 5 n 5 ARG 5 A CYS 6 n 6 CYS 6 A GLU 7 n 7 GLU 7 A LEU 8 n 8 LEU 8 A ALA 9 n 9 ALA 9 A ARG 10 n 10 ARG 10 A THR 11 n 11 THR 11 A LEU 12 n 12 LEU 12 A LYS 13 n 13 LYS 13 A ARG 14 n 14 ARG 14 A LEU 15 n 15 LEU 15 A GLY 16 n 16 GLY 16 A MET 17 n 17 MET 17 A ASP 18 n 18 ASP 18 A GLY 19 n 19 GLY 19 A TYR 20 n 20 TYR 20 A ARG 21 n 21 ARG 21 A GLY 22 n 22 GLY 22 A ILE 23 n 23 ILE 23 A SER 24 n 24 SER 24 A LEU 25 n 25 LEU 25 A ALA 26 n 26 ALA 26 A ASN 27 n 27 ASN 27 A TRP 28 n 28 TRP 28 A MET 29 n 29 MET 29 A CYS 30 n 30 CYS 30 A LEU 31 n 31 LEU 31 A ALA 32 n 32 ALA 32 A LYS 33 n 33 LYS 33 A TRP 34 n 34 TRP 34 A GLU 35 n 35 GLU 35 A SER 36 n 36 SER 36 A GLY 37 n 37 GLY 37 A TYR 38 n 38 TYR 38 A ASN 39 n 39 ASN 39 A THR 40 n 40 THR 40 A ARG 41 n 41 ARG 41 A ALA 42 n 42 ALA 42 A THR 43 n 43 THR 43 A ASN 44 n 44 ASN 44 A TYR 45 n 45 TYR 45 A ASN 46 n 46 ASN 46 A ALA 47 n 47 ALA 47 A GLY 48 n 48 GLY 48 A ASP 49 n 49 ASP 49 A ARG 50 n 50 ARG 50 A SER 51 n 51 SER 51 A THR 52 n 52 THR 52 A ASP 53 n 53 ASP 53 A TYR 54 n 54 TYR 54 A GLY 55 n 55 GLY 55 A ILE 56 n 56 ILE 56 A PHE 57 n 57 PHE 57 A GLN 58 n 58 GLN 58 A ILE 59 n 59 ILE 59 A ASN 60 n 60 ASN 60 A SER 61 n 61 SER 61 A ARG 62 n 62 ARG 62 A TYR 63 n 63 TYR 63 A TRP 64 n 64 TRP 64 A CYS 65 n 65 CYS 65 A ASN 66 n 66 ASN 66 A ASP 67 n 67 ASP 67 A GLY 68 n 68 GLY 68 A LYS 69 n 69 LYS 69 A THR 70 n 70 THR 70 A PRO 71 n 71 PRO 71 A GLY 72 n 72 GLY 72 A ALA 73 n 73 ALA 73 A VAL 74 n 74 VAL 74 A ASN 75 n 75 ASN 75 A ALA 76 n 76 ALA 76 A CYS 77 n 77 CYS 77 A HIS 78 n 78 HIS 78 A LEU 79 n 79 LEU 79 A SER 80 n 80 SER 80 A CYS 81 n 81 CYS 81 A SER 82 n 82 SER 82 A ALA 83 n 83 ALA 83 A LEU 84 n 84 LEU 84 A LEU 85 n 85 LEU 85 A GLN 86 n 86 GLN 86 A ASP 87 n 87 ASP 87 A ASN 88 n 88 ASN 88 A ILE 89 n 89 ILE 89 A ALA 90 n 90 ALA 90 A ASP 91 n 91 ASP 91 A ALA 92 n 92 ALA 92 A VAL 93 n 93 VAL 93 A ALA 94 n 94 ALA 94 A CYS 95 n 95 CYS 95 A ALA 96 n 96 ALA 96 A LYS 97 n 97 LYS 97 A ARG 98 n 98 ARG 98 A VAL 99 n 99 VAL 99 A VAL 100 n 100 VAL 100 A ARG 101 n 101 ARG 101 A ASP 102 n 102 ASP 102 A PRO 103 n 103 PRO 103 A GLN 104 n 104 GLN 104 A GLY 105 n 105 GLY 105 A ILE 106 n 106 ILE 106 A ARG 107 n 107 ARG 107 A ALA 108 n 108 ALA 108 A PHE 109 n 109 PHE 109 A VAL 110 n 110 VAL 110 A ALA 111 n 111 ALA 111 A TRP 112 n 112 TRP 112 A ARG 113 n 113 ARG 113 A ASN 114 n 114 ASN 114 A ARG 115 n 115 ARG 115 A CYS 116 n 116 CYS 116 A GLN 117 n 117 GLN 117 A ASN 118 n 118 ASN 118 A ARG 119 n 119 ARG 119 A ASP 120 n 120 ASP 120 A VAL 121 n 121 VAL 121 A ARG 122 n 122 ARG 122 A GLN 123 n 123 GLN 123 A TYR 124 n 124 TYR 124 A VAL 125 n 125 VAL 125 A GLN 126 n 126 GLN 126 A GLY 127 n 127 GLY 127 A CYS 128 n 128 CYS 128 A GLY 129 n 129 GLY 129 A VAL 130 n 130 VAL 130 A author_defined_assembly 1 monomeric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 A O ASN 44 A O ASN 44 A N ASP 53 A N ASP 53 15.74 0.22 0.18 0.18 1.60 8.0 12447 10. 1 3. MOLECULAR REPLACEMENT PDB ENTRY 1LZ1 0.2 1.60 8.0 85 1119 8 0 1026 0.008 1.490 24.36 1.270 1.60 14.8 1JKC 14328 0.0 0.05 1 5.1 91.2 data collection MADNES model building X-PLOR refinement X-PLOR data reduction MADNES phasing X-PLOR HUMAN LYSOZYME MUTANT WITH TRP 109 REPLACED BY PHE 1 N N 2 N N 2 N N 3 N N A ARG 5 A ARG 5 HELX_P A ARG 14 A ARG 14 1 1 10 A TYR 20 A TYR 20 HELX_P A GLY 22 A GLY 22 5 2 3 A LEU 25 A LEU 25 HELX_P A SER 36 A SER 36 1 3 12 A CYS 81 A CYS 81 HELX_P A LEU 85 A LEU 85 5 4 5 A ALA 90 A ALA 90 HELX_P A ARG 101 A ARG 101 1 5 12 A GLY 105 A GLY 105 HELX_P A ALA 108 A ALA 108 5 6 4 A VAL 110 A VAL 110 HELX_P A ARG 115 A ARG 115 1 7 6 A ARG 122 A ARG 122 HELX_P A TYR 124 A TYR 124 5 8 3 disulf 2.029 A CYS 6 A SG CYS 6 1_555 A CYS 128 A SG CYS 128 1_555 disulf 2.011 A CYS 30 A SG CYS 30 1_555 A CYS 116 A SG CYS 116 1_555 disulf 2.041 A CYS 65 A SG CYS 65 1_555 A CYS 81 A SG CYS 81 1_555 disulf 2.027 A CYS 77 A SG CYS 77 1_555 A CYS 95 A SG CYS 95 1_555 LYSOZYME HYDROLASE, MURAMIDASE, HYDROLASE (O-GLYCOSYL), GLYCOSIDASE, LYSOZYME LYSC_HUMAN UNP 1 1 P61626 MKALIVLGLVLLSVTVQGKVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSR YWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQYVQGCGV 19 148 1JKC 1 130 P61626 A 1 1 130 1 TRP engineered mutation PHE 109 1JKC A P61626 UNP 127 109 2 anti-parallel A THR 43 A THR 43 A ASN 46 A ASN 46 A SER 51 A SER 51 A TYR 54 A TYR 54 BINDING SITE FOR RESIDUE NO3 A 131 A NO3 131 Software 5 BINDING SITE FOR RESIDUE NO3 A 132 A NO3 132 Software 6 A GLU 4 A GLU 4 5 1_555 A ARG 5 A ARG 5 5 1_555 A CYS 6 A CYS 6 5 1_555 A GLU 7 A GLU 7 5 1_555 A HOH 159 D HOH 5 1_555 A ASN 27 A ASN 27 6 1_555 A ASN 66 A ASN 66 6 4_557 A ASN 75 A ASN 75 6 4_557 A SER 80 A SER 80 6 4_557 A HOH 134 D HOH 6 4_557 A HOH 145 D HOH 6 1_555 19 P 21 21 21