0.037193 0.000000 0.000000 0.000000 0.037965 0.000000 0.000000 0.000000 0.049290 0.000000 0.000000 0.000000 Vitagliano, L. Berisio, R. Mazzarella, L. Zagari, A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 26.887 26.340 20.288 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 N N 2 N C N 3 N C N 4 N O N 5 N O N 6 N H N 7 N H N 8 N H N 9 N H N 10 N H N 11 N O N 12 N H N 13 N H N 14 N N N 15 S C N 16 N C N 17 N O N 18 N C N 19 N C N 20 N C N 21 N O N 22 N H N 23 N H N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N doub 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 sing N 15 N sing N 16 N sing N 17 N sing N 18 N doub 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 sing N 26 N sing N 27 N sing N 28 N sing US Biopolymers BIPMAA 0161 0006-3525 58 459 464 10.1002/1097-0282(20010415)58:5<459::AID-BIP1021>3.0.CO;2-V 11241217 Structural bases of collagen stabilization induced by proline hydroxylation. 2001 DK Acta Crystallogr.,Sect.D ABCRE6 0766 0907-4449 56 55 61 10.1107/S0907444999014158 Effects of microgravity on the crystal quality of a collagen-like polypeptide 2000 UK J.Mol.Biol. JMOBAK 0070 0022-2836 280 623 638 10.1006/jmbi.1998.1881 X-RAY CRYSTALLOGRAPHIC DETERMINATION OF A COLLAGEN-LIKE PEPTIDE WITH THE REPEATING SEQUENCE (PRO-PRO-GLY) 1998 10.2210/pdb1g9w/pdb pdb_00001g9w 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 293 1 IMAGE PLATE 1998-12-01 MARRESEARCH SINGLE WAVELENGTH M x-ray 1 1.004 1.0 5.2R ELETTRA 1.004 SYNCHROTRON ELETTRA BEAMLINE 5.2R 771.859 COLLAGEN-LIKE PEPTIDE 1 syn polymer 520.578 COLLAGEN-LIKE PEPTIDE 2 syn polymer 18.015 water 36 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 1.97 37.43 DIALYSIS SODIUM ACETATE, ACETIC ACID, DIALYSIS, temperature 293K 293 chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model repository Initial release Version format compliance Version format compliance Data collection Database references Refinement description 1 0 2001-04-18 1 1 2008-04-27 1 2 2011-07-13 1 3 2024-02-07 1 4 2024-04-03 _database_2.pdbx_DOI _database_2.pdbx_database_accession RCSB Y RCSB 2000-11-28 REL 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. 1A3J PDB experimental model HOH 1001 3 HOH HOH 1001 A HOH 1002 3 HOH HOH 1002 A HOH 1003 3 HOH HOH 1003 A HOH 1004 3 HOH HOH 1004 A HOH 1005 3 HOH HOH 1005 A HOH 1006 3 HOH HOH 1006 A HOH 1007 3 HOH HOH 1007 A HOH 1008 3 HOH HOH 1008 A HOH 1009 3 HOH HOH 1009 A HOH 1022 3 HOH HOH 1022 A HOH 1023 3 HOH HOH 1023 A HOH 1024 3 HOH HOH 1024 A HOH 1025 3 HOH HOH 1025 A HOH 1026 3 HOH HOH 1026 A HOH 1028 3 HOH HOH 1028 A HOH 1030 3 HOH HOH 1030 A HOH 1034 3 HOH HOH 1034 A HOH 1036 3 HOH HOH 1036 A HOH 1037 3 HOH HOH 1037 A HOH 1010 3 HOH HOH 1010 B HOH 1011 3 HOH HOH 1011 B HOH 1012 3 HOH HOH 1012 B HOH 1013 3 HOH HOH 1013 B HOH 1014 3 HOH HOH 1014 B HOH 1021 3 HOH HOH 1021 B HOH 1029 3 HOH HOH 1029 B HOH 1035 3 HOH HOH 1035 B HOH 1015 3 HOH HOH 1015 C HOH 1016 3 HOH HOH 1016 C HOH 1017 3 HOH HOH 1017 C HOH 1018 3 HOH HOH 1018 C HOH 1019 3 HOH HOH 1019 C HOH 1020 3 HOH HOH 1020 C HOH 1027 3 HOH HOH 1027 C HOH 1031 3 HOH HOH 1031 C HOH 1032 3 HOH HOH 1032 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 0.1460000 0.1470000 0.1900000 0.1940000 20 20 309 author_and_software_defined_assembly PISA 3 trimeric 1020 -7 1540 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 A B N C PRO GLY 1 36 1.30 1_555 1_556 1 B C N C PRO GLY 31 66 1.34 1_555 1_556 1 A C C N GLY PRO 9 61 1.34 1_555 1_554 DUE TO THE QUASI-INFINITE 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. 0.1940000 0.1470000 1.30 10.00 147 320 179 20 89.0 RANDOM 1 THROUGHOUT 0 PDB1A3J.ENT ENGH AND HUBER 162. 1.30 10.00 36 162 0 0 126 0.015 0.026 1.3 15 1G9W 3448 0.0420000 1 4.8 89.0 0.0930000 1.3 1.33 66.4 refinement SHELXL-97 data reduction DENZO data scaling SCALEPACK STRUCTURAL BASIS OF COLLAGEN STABILIZATION INDUCED BY PROLINE HYDROXYLATION 1 N N 2 N N 2 N N 3 N N 3 N N 3 N N THE 21 RESIDUE ASYMMETRIC UNIT CORRESPONDS TO ONE TRIPLE-HELICAL REPEAT AND IS SMALLER THAN THE ENTIRE 90 RESIDUE PEPTIDE. 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. STRUCTURAL PROTEIN COLLAGEN, EXTRACELLULAR MATRIX, STRUCTURAL PROTEIN 1G9W PDB 1 1G9W 1G9W PDB 2 1G9W 1 9 1G9W 1 9 1G9W A 1 1 9 31 36 1G9W 31 36 1G9W B 2 1 6 61 66 1G9W 61 66 1G9W C 2 1 6 19 P 21 21 21