0.037286 0.000000 0.000000 0.000000 0.038037 0.000000 0.000000 0.000000 0.049554 0.00000 0.00000 0.00000 Kramer, R.Z. Vitagliano, L. Bella, J. Berisio, R. Mazzarella, L. Brodsky, B. Zagari, A. Berman, H.M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 26.820 26.290 20.180 C2 H4 O2 60.052 ACETIC ACID non-polymer C2 H5 N O2 75.067 y GLYCINE peptide linking H2 O 18.015 WATER non-polymer C5 H9 N O2 115.130 y PROLINE L-peptide linking N 1 N C N 2 N O N 3 N O N 4 N C N 5 N H N 6 N H N 7 N H N 8 N H N 9 N N N 10 N C N 11 N C N 12 N O N 13 N O N 14 N H N 15 N H N 16 N H N 17 N H N 18 N H N 19 N O N 20 N H N 21 N H N 22 N N N 23 S C N 24 N C N 25 N O N 26 N C N 27 N C N 28 N C N 29 N O N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 1 N doub N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N doub N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N doub N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N sing N 34 N sing N 35 N sing UK J.Mol.Biol. JMOBAK 0070 0022-2836 280 623 638 10.1006/jmbi.1998.1881 9677293 X-ray crystallographic determination of a collagen-like peptide with the repeating sequence (Pro-Pro-Gly). 1998 10.2210/pdb1a3i/pdb pdb_00001a3i 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 0.00000 0.00000 20.18000 259.0 1 DIFFRACTOMETER 1991-10 ENRAF-NONIUS FAST M x-ray 1 1.5418 1.0 1.5418 771.859 COLLAGEN-LIKE PEPTIDE 1 man polymer 520.578 COLLAGEN-LIKE PEPTIDE 2 man polymer 60.052 ACETIC ACID 2 syn non-polymer 18.015 water 37 nat water no no PPGPPGPPG PPGPPGPPG A polypeptide(L) no no PPGPPG PPGPPG B,C polypeptide(L) n n n n n n n n n n n n n n n 1 1.95 36.82 PEPTIDE WAS CRYSTALLIZED FROM 4.0 MG/ML PEPTIDE IN 10% ACETIC ACID, 0.1% SODIUM AZIDE, AND 3.0% PEG400. diffrn_detector pdbx_database_status chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model struct_conn struct_site repository Initial release Version format compliance Version format compliance Data collection Other Data collection Database references Derived calculations Refinement description 1 0 1998-05-06 1 1 2008-03-24 1 2 2011-07-13 1 3 2018-04-18 1 4 2024-04-03 _diffrn_detector.detector _pdbx_database_status.process_site _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_symmetry _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Y BNL 1998-01-22 REL REL ACY ACETIC ACID HOH water HYDROGEN BONDS BETWEEN PEPTIDE CHAINS FOLLOW THE RICH AND CRICK MODEL II FOR COLLAGEN. FOR EACH CHAIN, RESIDUE NUMBERING CORRESPONDS TO THE ENTIRE MOLECULE RATHER THAN THE SHORTER ASYMMETRIC UNIT. IDEALIZED SEVEN-FOLD TRIPLE-HELIX Other in silico model ACY 401 3 ACY ACY 401 A ACY 402 3 ACY ACY 402 C HOH 101 4 HOH HOH 101 A HOH 102 4 HOH HOH 102 A HOH 103 4 HOH HOH 103 A HOH 104 4 HOH HOH 104 A HOH 105 4 HOH HOH 105 A HOH 106 4 HOH HOH 106 A HOH 107 4 HOH HOH 107 A HOH 108 4 HOH HOH 108 A HOH 109 4 HOH HOH 109 A HOH 201 4 HOH HOH 201 A HOH 204 4 HOH HOH 204 A HOH 209 4 HOH HOH 209 A HOH 218 4 HOH HOH 218 A HOH 220 4 HOH HOH 220 A HOH 241 4 HOH HOH 241 A HOH 244 4 HOH HOH 244 A HOH 245 4 HOH HOH 245 A HOH 111 4 HOH HOH 111 B HOH 112 4 HOH HOH 112 B HOH 113 4 HOH HOH 113 B HOH 115 4 HOH HOH 115 B HOH 116 4 HOH HOH 116 B HOH 242 4 HOH HOH 242 B HOH 246 4 HOH HOH 246 B HOH 247 4 HOH HOH 247 B HOH 121 4 HOH HOH 121 C HOH 122 4 HOH HOH 122 C HOH 123 4 HOH HOH 123 C HOH 124 4 HOH HOH 124 C HOH 125 4 HOH HOH 125 C HOH 126 4 HOH HOH 126 C HOH 202 4 HOH HOH 202 C HOH 205 4 HOH HOH 205 C HOH 208 4 HOH HOH 208 C HOH 210 4 HOH HOH 210 C HOH 243 4 HOH HOH 243 C HOH 248 4 HOH HOH 248 C PRO 1 n 1 PRO 1 A PRO 2 n 2 PRO 2 A GLY 3 n 3 GLY 3 A PRO 4 n 4 PRO 4 A PRO 5 n 5 PRO 5 A GLY 6 n 6 GLY 6 A PRO 7 n 7 PRO 7 A PRO 8 n 8 PRO 8 A GLY 9 n 9 GLY 9 A PRO 31 n 1 PRO 31 B PRO 32 n 2 PRO 32 B GLY 33 n 3 GLY 33 B PRO 34 n 4 PRO 34 B PRO 35 n 5 PRO 35 B GLY 36 n 6 GLY 36 B PRO 61 n 1 PRO 61 C PRO 62 n 2 PRO 62 C GLY 63 n 3 GLY 63 C PRO 64 n 4 PRO 64 C PRO 65 n 5 PRO 65 C GLY 66 n 6 GLY 66 C author_defined_assembly 15 pentadecameric 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 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_556 x,y,z+1 crystal symmetry operation 0.0000000000 0.0000000000 20.1800000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_557 x,y,z+2 crystal symmetry operation 0.0000000000 0.0000000000 40.3600000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_558 x,y,z+3 crystal symmetry operation 0.0000000000 0.0000000000 60.5400000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_559 x,y,z+4 crystal symmetry operation 0.0000000000 0.0000000000 80.7200000000 1 A PRO 2 -56.35 171.52 1 A PRO 5 -47.11 164.30 PARHCSDX.PRO TOPHCSDX.PRO 15.9 DUE TO THE QUASI-INFINITE, AVERAGED NATURE OF THE TRIPLE HELIX, DURING REFINEMENT COVALENT BONDS ARE NECESSARY TO JOIN THE MOLECULE WITH ITS SYMMETRY MATES BOTH ABOVE IT AND BELOW IT ALONG THE HELICAL AXIS AND TIGHT REFINEMENT CONSTRAINTS WERE MAINTAINED. THE UNIT CELL AXES WERE CHOSEN TO COINCIDE WITH A PREVIOUS STRUCTURE DETERMINATION (OKUYAMA 1981) OF THIS PEPTIDE. 0.1810000 0.1810000 1.97 8. 861 76.7 1000000. 0.1 1 GROUP 2. MOLECULAR REPLACEMENT IDEALIZED SEVEN-FOLD TRIPLE-HELIX 1.97 8. 45 171 0 0 126 0.01 2.07 2.11 0.2200000 2.04 69 10 63.3 1.97 1A3I 1136 0. 1 99.5 1.97 2.2 98. model building X-PLOR 3.1 refinement LALS data reduction MOLEN phasing X-PLOR 3.1 refinement X-PLOR X-RAY CRYSTALLOGRAPHIC DETERMINATION OF A COLLAGEN-LIKE PEPTIDE WITH THE REPEATING SEQUENCE (PRO-PRO-GLY) 1 N N 2 N N 2 N N 3 N N 3 N N 4 N N 4 N N 4 N N THE 21 RESIDUE ASYMMETRIC UNIT CORRESPONDS TO ONE TRIPLE-HELICAL REPEAT AND IS SMALLER THAN THE ENTIRE 90 RESIDUE PEPTIDE DUE TO TRANSLATIONAL DISORDER ALONG THE HELICAL AXIS. THE RESULT IS A POLYMER-LIKE STRUCTURE WITH NO DEFINED ENDS. THE POLYMER STRUCTURE IS FORMED BY CONTINUATION OF THE CHAINS USING THE SYMMETRY-RELATED MOLECULES ALONG THE HELICAL AXIS. THE TVECT RECORD BELOW PRESENTS THE TRANSLATION THAT WILL GENERATE THE POLYMER. NOTE: THEREFORE, CLOSE CONTACTS BETWEEN SYMMETRY-RELATED MOLECULES ARE INTENTIONAL AND NECESSARY. INTERCHAIN HYDROGEN BONDING AT THE END OF CHAINS ALSO UTILIZES SYMMETRY-RELATED MOLECULES. THE ENTIRE 30 RESIDUE LONG PEPTIDE CAN BE GENERATED FROM THE SUBMITTED ASYMMETRIC UNIT BY APPLYING THE FOLLOWING TRANSLATIONS (USING FRACTIONAL COORDINATES): CHAIN A: TRANSLATE RESIDUES 1 - 9 BY (0 0 1), (0 0 2), AND (0 0 3) AND RESIDUES 7 - 9 BY (0 0 4). CHAIN B: TRANSLATE RESIDUES 31 - 36 BY (0 0 1), (0 0 2), AND (0 0 3). CHAIN C: TRANSLATE RESIDUES 61 - 66 BY (0 0 1), (0 0 2), AND (0 0 3) AND RESIDUES 64 - 66 BY (004). THIS WILL RESULT IN A MOLECULE WITH A TOTAL OF 90 RESIDUES, 30 IN EACH CHAIN. covale 1.340 both A PRO 1 A N PRO 1 1_555 B GLY 36 B C GLY 6 1_556 covale 1.309 both A GLY 9 A C GLY 9 1_556 C PRO 61 C N PRO 1 1_555 covale 1.328 both B PRO 31 B N PRO 1 1_555 C GLY 66 C C GLY 6 1_556 EXTRACELLULAR MATRIX COLLAGEN, EXTRACELLULAR MATRIX 1A3I PDB 1 1A3I 1A3I PDB 2 1A3I 1 9 1A3I 1 9 1A3I A 1 1 9 31 36 1A3I 31 36 1A3I B 2 1 6 61 66 1A3I 61 66 1A3I C 2 1 6 BINDING SITE FOR RESIDUE ACY A 401 A ACY 401 Software 7 BINDING SITE FOR RESIDUE ACY C 402 C ACY 402 Software 5 A PRO 5 A PRO 5 7 1_555 A PRO 8 A PRO 8 7 2_575 A HOH 103 F HOH 7 1_555 A HOH 218 F HOH 7 1_555 C PRO 64 C PRO 4 7 4_466 C HOH 122 H HOH 7 4_466 C ACY 402 E ACY 7 4_466 A ACY 401 D ACY 5 4_566 B PRO 34 B PRO 4 5 4_566 B HOH 247 G HOH 5 4_566 C HOH 122 H HOH 5 1_555 C HOH 202 H HOH 5 1_555 19 P 21 21 21