0.022366 0.012913 0.000000 0.000000 0.025826 0.000000 0.000000 0.000000 0.010254 0.00000 0.00000 0.00000 Ratnaparkhi, G.S. Varadarajan, R. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.00 90.00 120.00 44.710 44.710 97.520 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 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 C3 H8 N2 O2 104.108 n AMINOSERINE L-peptide linking O4 S -2 96.063 SULFATE ION non-polymer C4 H9 N O3 119.119 y THREONINE 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 Biochemistry BICHAW 0033 0006-2960 39 12365 12374 10.1021/bi000775k 11015216 Thermodynamic and structural studies of cavity formation in proteins suggest that loss of packing interactions rather than the hydrophobic effect dominates the observed energetics. 2000 US Proteins: Struct.,Funct.,Genet. PSFGEY 0867 0887-3585 36 282 294 10.1002/(SICI)1097-0134(19990815)36:3<282::AID-PROT3>3.3.CO;2-6 X-ray crystallographic studies of the denaturation of ribonuclease S 1999 US Biochemistry BICHAW 0033 0006-2960 31 12315 12327 Crystallographic structures of ribonuclease S variants with nonpolar substitution at position 13: packing and cavities 1992 US Biochemistry BICHAW 0033 0006-2960 33 8587 8593 Thermodynamic and structural consequences of changing a sulfur atom to a methylene group in the M13Nle mutation in ribonuclease-S 1994 1.000000 .000000 .000000 .000000 1.000000 .000000 .000000 .000000 1.000000 .00000 .00000 .00000 293 1 AREA DETECTOR 1994-03-08 XENTRONICS SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU SYNTHETIC 1675.863 S PEPTIDE RESIDUES 1-15 F8A 1 syn polymer 11294.749 RNASE S RESIDUES 24-124 1 nat polymer 96.063 SULFATE ION 1 syn non-polymer 18.015 water 35 nat water no yes KETAAAKAERQHMD(SET) KETAAAKAERQHMDS A polypeptide(L) no no NYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQAN KHIIVACEGNPYVPVHFDASV NYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQAN KHIIVACEGNPYVPVHFDASV B 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 cattle DERIEVED FROM A LIMIT DIGEST OF BOVINE PANCREATIC RNASE A Bos sample 9913 Bos taurus 1 2.17 43.28 VAPOR DIFFUSION, SITTING DROP 5.75 3M CsCl, 35% Ammonium Sulfate. 0.1 M Sodium Acetate, pH 5.75, VAPOR DIFFUSION, SITTING DROP, temperature 20K 293.0 software exptl_crystal_grow struct_ref_seq_dif repository Initial release Version format compliance Version format compliance Structure summary Refinement description Experimental preparation Database references 1 0 1999-10-20 1 1 2008-04-27 1 2 2011-07-13 1 3 2017-02-01 1 4 2017-10-04 1 5 2018-01-31 1 6 2018-03-14 _exptl_crystal_grow.temp _struct_ref_seq_dif.details Control structure for this study, RNase S15. RELATED STUDY RELATED STUDY RCSB Y RCSB 1999-10-07 REL REL SO4 SULFATE ION HOH water S15 peptide synthesized by solid phase peptide synthesis sample SO4 125 3 SO4 SO4 125 B HOH 202 4 HOH HOH 202 A HOH 218 4 HOH HOH 218 A HOH 227 4 HOH HOH 227 A HOH 236 4 HOH HOH 236 A HOH 245 4 HOH HOH 245 A HOH 247 4 HOH HOH 247 A HOH 201 4 HOH HOH 201 B HOH 203 4 HOH HOH 203 B HOH 205 4 HOH HOH 205 B HOH 207 4 HOH HOH 207 B HOH 208 4 HOH HOH 208 B HOH 209 4 HOH HOH 209 B HOH 210 4 HOH HOH 210 B HOH 211 4 HOH HOH 211 B HOH 212 4 HOH HOH 212 B HOH 213 4 HOH HOH 213 B HOH 214 4 HOH HOH 214 B HOH 215 4 HOH HOH 215 B HOH 216 4 HOH HOH 216 B HOH 217 4 HOH HOH 217 B HOH 219 4 HOH HOH 219 B HOH 221 4 HOH HOH 221 B HOH 222 4 HOH HOH 222 B HOH 226 4 HOH HOH 226 B HOH 228 4 HOH HOH 228 B HOH 237 4 HOH HOH 237 B HOH 241 4 HOH HOH 241 B HOH 243 4 HOH HOH 243 B HOH 248 4 HOH HOH 248 B HOH 252 4 HOH HOH 252 B HOH 255 4 HOH HOH 255 B HOH 257 4 HOH HOH 257 B HOH 259 4 HOH HOH 259 B HOH 260 4 HOH HOH 260 B HOH 262 4 HOH HOH 262 B LYS 1 n 1 LYS 1 A GLU 2 n 2 GLU 2 A THR 3 n 3 THR 3 A ALA 4 n 4 ALA 4 A ALA 5 n 5 ALA 5 A ALA 6 n 6 ALA 6 A LYS 7 n 7 LYS 7 A ALA 8 n 8 ALA 8 A GLU 9 n 9 GLU 9 A ARG 10 n 10 ARG 10 A GLN 11 n 11 GLN 11 A HIS 12 n 12 HIS 12 A MET 13 n 13 MET 13 A ASP 14 n 14 ASP 14 A SET 15 n 15 SET 15 A ASN 24 n 1 ASN 24 B TYR 25 n 2 TYR 25 B CYS 26 n 3 CYS 26 B ASN 27 n 4 ASN 27 B GLN 28 n 5 GLN 28 B MET 29 n 6 MET 29 B MET 30 n 7 MET 30 B LYS 31 n 8 LYS 31 B SER 32 n 9 SER 32 B ARG 33 n 10 ARG 33 B ASN 34 n 11 ASN 34 B LEU 35 n 12 LEU 35 B THR 36 n 13 THR 36 B LYS 37 n 14 LYS 37 B ASP 38 n 15 ASP 38 B ARG 39 n 16 ARG 39 B CYS 40 n 17 CYS 40 B LYS 41 n 18 LYS 41 B PRO 42 n 19 PRO 42 B VAL 43 n 20 VAL 43 B ASN 44 n 21 ASN 44 B THR 45 n 22 THR 45 B PHE 46 n 23 PHE 46 B VAL 47 n 24 VAL 47 B HIS 48 n 25 HIS 48 B GLU 49 n 26 GLU 49 B SER 50 n 27 SER 50 B LEU 51 n 28 LEU 51 B ALA 52 n 29 ALA 52 B ASP 53 n 30 ASP 53 B VAL 54 n 31 VAL 54 B GLN 55 n 32 GLN 55 B ALA 56 n 33 ALA 56 B VAL 57 n 34 VAL 57 B CYS 58 n 35 CYS 58 B SER 59 n 36 SER 59 B GLN 60 n 37 GLN 60 B LYS 61 n 38 LYS 61 B ASN 62 n 39 ASN 62 B VAL 63 n 40 VAL 63 B ALA 64 n 41 ALA 64 B CYS 65 n 42 CYS 65 B LYS 66 n 43 LYS 66 B ASN 67 n 44 ASN 67 B GLY 68 n 45 GLY 68 B GLN 69 n 46 GLN 69 B THR 70 n 47 THR 70 B ASN 71 n 48 ASN 71 B CYS 72 n 49 CYS 72 B TYR 73 n 50 TYR 73 B GLN 74 n 51 GLN 74 B SER 75 n 52 SER 75 B TYR 76 n 53 TYR 76 B SER 77 n 54 SER 77 B THR 78 n 55 THR 78 B MET 79 n 56 MET 79 B SER 80 n 57 SER 80 B ILE 81 n 58 ILE 81 B THR 82 n 59 THR 82 B ASP 83 n 60 ASP 83 B CYS 84 n 61 CYS 84 B ARG 85 n 62 ARG 85 B GLU 86 n 63 GLU 86 B THR 87 n 64 THR 87 B GLY 88 n 65 GLY 88 B SER 89 n 66 SER 89 B SER 90 n 67 SER 90 B LYS 91 n 68 LYS 91 B TYR 92 n 69 TYR 92 B PRO 93 n 70 PRO 93 B ASN 94 n 71 ASN 94 B CYS 95 n 72 CYS 95 B ALA 96 n 73 ALA 96 B TYR 97 n 74 TYR 97 B LYS 98 n 75 LYS 98 B THR 99 n 76 THR 99 B THR 100 n 77 THR 100 B GLN 101 n 78 GLN 101 B ALA 102 n 79 ALA 102 B ASN 103 n 80 ASN 103 B LYS 104 n 81 LYS 104 B HIS 105 n 82 HIS 105 B ILE 106 n 83 ILE 106 B ILE 107 n 84 ILE 107 B VAL 108 n 85 VAL 108 B ALA 109 n 86 ALA 109 B CYS 110 n 87 CYS 110 B GLU 111 n 88 GLU 111 B GLY 112 n 89 GLY 112 B ASN 113 n 90 ASN 113 B PRO 114 n 91 PRO 114 B TYR 115 n 92 TYR 115 B VAL 116 n 93 VAL 116 B PRO 117 n 94 PRO 117 B VAL 118 n 95 VAL 118 B HIS 119 n 96 HIS 119 B PHE 120 n 97 PHE 120 B ASP 121 n 98 ASP 121 B ALA 122 n 99 ALA 122 B SER 123 n 100 SER 123 B VAL 124 n 101 VAL 124 B author_and_software_defined_assembly PISA 2 dimeric 1730 -22 6460 A SET 15 AMINOSERINE A SET 15 SER 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 B N PHE 46 B N PHE 23 B O THR 82 B O THR 59 B O ARG 85 B O ARG 62 B N LYS 98 B N LYS 75 B N VAL 63 B N VAL 40 B O CYS 72 B O CYS 49 B N TYR 73 B N TYR 50 B O VAL 108 B O VAL 85 B N GLU 111 B N GLU 88 B O VAL 116 B O VAL 93 1 B B HE22 H1 GLN HOH 60 216 1.30 1 B TYR 92 -16.74 1 B B TYR PRO 92 93 -95.37 1 9.82 1.40 123.60 133.42 B B B CD NE CZ ARG ARG ARG 85 85 85 N 1 9.71 0.50 120.30 130.01 B B B NE CZ NH1 ARG ARG ARG 85 85 85 N 1 -5.38 0.50 120.30 114.92 B B B NE CZ NH2 ARG ARG ARG 85 85 85 N 1 16.65 2.00 110.40 127.05 B B B CB CA C TYR TYR TYR 92 92 92 N 1 -5.05 0.60 121.00 115.95 B B B CB CG CD2 TYR TYR TYR 92 92 92 N 1 4.44 0.60 121.00 125.44 B B B CB CG CD1 TYR TYR TYR 92 92 92 N 1 13.96 1.50 119.30 133.26 B B B C N CA TYR PRO PRO 92 93 93 Y 1 -16.10 2.10 128.40 112.30 B B B C N CD TYR PRO PRO 92 93 93 Y 1 10.73 1.20 103.30 114.03 B B B N CA CB PRO PRO PRO 93 93 93 N 1 B B CG CD1 TYR TYR 92 92 0.083 0.013 1.387 1.470 N 1 B B O O HOH HOH 252 255 0.40 1_555 3_554 1 B B H2 O HOH HOH 252 255 0.59 1_555 3_554 1 B B O H2 HOH HOH 252 255 0.69 1_555 3_554 1 B B H1 H1 HOH HOH 252 255 0.89 1_555 3_554 1 A B HZ1 H1 LYS HOH 1 214 0.90 1_555 6_455 1 A B HZ1 O LYS HOH 1 214 0.96 1_555 6_455 1 B B H1 H2 HOH HOH 252 255 0.96 1_555 3_554 1 B B H1 O HOH HOH 252 255 1.02 1_555 3_554 1 B B O H1 HOH HOH 252 255 1.03 1_555 3_554 1 B B H2 H1 HOH HOH 252 255 1.19 1_555 3_554 1 A B NZ O LYS HOH 1 214 1.40 1_555 6_455 1 A B HZ2 O LYS HOH 1 214 1.50 1_555 6_455 1 B ARG 39 170.77 165.19 1 B HIS 48 -92.67 50.12 1 B CYS 58 -64.27 3.20 1 B GLN 60 -100.20 -131.42 1 B ASN 67 -65.72 2.21 1 B TYR 92 -27.95 170.11 1 B PRO 93 -8.70 -43.30 1 B ALA 122 177.50 -173.34 1 B SER 123 -165.49 110.64 PARHCSDX_RV.PRO TOPHCSDX.PRO PARAM19.SOL TOPH.SO4 TOPH19X_WAT.PRO 13.9 .00 .00 .00 .00 .00 .00 NA 0.257 .012 0.21 0.21 0.21 2.25 10.00 557 5238 10.6 92.3 RANDOM 10000000.00 .00 1 RESTRAINED THROUGHOUT 1.0 NA .34 .30 3.80 .35 .28 2.25 10.00 35 939 5 0 899 .028 2.8 25.2 6.50 1.82 1.50 2.87 2.00 5.62 2.00 9.64 2.50 0.385 .049 0.305 2.37 62 504 7 11.0 69.8 22.3 2.2 10 1D5H 5328 1 1 0.06 1 13.0 2.5 95 0.3 2.25 2.37 504 1 70 data scaling X-GEN data reduction X-GEN model building X-PLOR refinement X-PLOR 3.851 phasing X-PLOR RNASE S COMPLEXED WITH S PEPTIDE Rnase s(f8a). mutant ribonucleasE S. 1 N N 2 N N 3 N N 4 N N 4 N N Monomer. Two fragments S peptide and S protein held together by non-covalent interactions A THR 3 A THR 3 HELX_P A MET 13 A MET 13 1 1 11 B ASN 24 B ASN 1 HELX_P B ARG 33 B ARG 10 1 2 10 B SER 50 B SER 27 HELX_P B ALA 56 B ALA 33 1 3 7 B VAL 57 B VAL 34 HELX_P B GLN 60 B GLN 37 5 4 4 disulf 2.032 B CYS 26 B SG CYS 3 1_555 B CYS 84 B SG CYS 61 1_555 disulf 2.008 B CYS 40 B SG CYS 17 1_555 B CYS 95 B SG CYS 72 1_555 disulf 1.788 B CYS 58 B SG CYS 35 1_555 B CYS 110 B SG CYS 87 1_555 disulf 1.994 B CYS 65 B SG CYS 42 1_555 B CYS 72 B SG CYS 49 1_555 covale 1.324 A ASP 14 A C ASP 14 1_555 A SET 15 A N SET 15 1_555 HYDROLASE RNASE S MUTANT F8A CAVITY S PROTEIN S PEPTIDE, HYDROLASE B ASN 113 B ASN 90 1 B PRO 114 B PRO 91 -0.15 RNAS1_BOVIN UNP 1 P61823 RNP_BOVIN UNP 2 P00656 1 15 1D5H 1 15 P61823 A 1 1 15 50 150 1D5H 24 124 P00656 B 2 1 101 1 PHE ENGINEERED MUTATION ALA 8 1D5H A P61823 UNP 8 8 3 4 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel B VAL 43 B VAL 20 B VAL 47 B VAL 24 B MET 79 B MET 56 B GLU 86 B GLU 63 B TYR 97 B TYR 74 B LYS 104 B LYS 81 B LYS 61 B LYS 38 B VAL 63 B VAL 40 B CYS 72 B CYS 49 B GLN 74 B GLN 51 B ILE 106 B ILE 83 B GLU 111 B GLU 88 B VAL 116 B VAL 93 B SER 123 B SER 100 BINDING SITE FOR RESIDUE SO4 B 125 Software 4 A HIS 12 A HIS 12 4 1_555 B HIS 119 B HIS 96 4 1_555 B PHE 120 B PHE 97 4 1_555 B HOH 215 E HOH 4 1_555 152 P 31 2 1