1. Topic 1 Roland Dunbrack

2. Modeling of Biological Units Model data files of single proteins may require –sequence alignment(s) to templates (entry and chain) –sequence-coordinate correspondence –methods description –information on ligands Models of biological units -- homo-N-mers, protein complexes, with ligands, ions, etc. would require more: –sequence alignments for each protein to templates –source of biological unit (RCSB or PQS) –which protein of model based on which chain of asymmetric unit and which symmetry operator used to build it –which ligands associated with which chains PDB format is inadequate We should use XML (preferably) or CIF, using same entity_ID/asym_ID/seq_id schema used by RCSB with additional tags specific for models of various types (e.g., for methods and target-template alignments)

3. The XML Files and Data Uniformity RCSB project to remake all the PDB files and set standards for all new files fixing format errors and completing information missing in many old files sequence-coordinate correspondence unique identifiers for all molecules and atoms no fixed width fields as in “PDB format” contents of XML files for experimental structures: –asymmetric unit contents –biological unit contents –covalent attachments and modified residues –non-covalent ligands, DNA, RNA –structural quality -- missing residues, resolution, R-factors, B-factors add modeling-specific tags –sequence alignments to template(s) –methods: alignment, coordinate-building, docking, refinement, assessment, etc. –asym_ID of model corresponding to asym_ID of templates+symmetry operator

4. ATOM C CB HIS A 1 3 52.555 45.674 100.990 1.00 19.69 3 HIS A CB 1 ATOM 3016 N MET B 99 46.065 47.943 69.114 1.00 11.54 N ATOM 3017 CA MET B 99 45.485 47.305 70.273 1.00 8.93 C ATOM 3018 C MET B 99 46.601 46.699 71.103 1.00 7.84 C ATOM 3019 O MET B 99 46.344 46.047 72.093 1.00 11.44 O ATOM 3020 CB MET B 99 44.560 46.193 69.855 1.00 10.44 C ATOM 3021 CG MET B 99 43.410 46.613 69.011 1.00 12.80 C ATOM 3022 SD MET B 99 42.376 45.219 68.545 1.00 18.72 S ATOM 3023 CE MET B 99 41.301 46.309 67.701 1.00 17.92 C ATOM 3024 OXT MET B 99 47.758 46.882 70.814 1.00 8.38 O

5. Entity 1 PBGS Molecule types Molecules in the asymmetric unit AsymID AAsymID B Entity 2 Levulinic acid AsymID CAsymID D Entity 3 Zn 2+ AsymID KAsymID L Entity 4 water AsymID W AsymID MAsymID N (res 1, res 2, res 3…)

6. AsymID W (res 1, res 2, res 3…) AsymID AAsymID B AsymID CAsymID D AsymID KAsymID L AsymID MAsymID N AsymID AAsymID B AsymID CAsymID D AsymID KAsymID L AsymID MAsymID N AsymID AAsymID B AsymID CAsymID D AsymID KAsymID L AsymID MAsymID N AsymID AAsymID B AsymID CAsymID D AsymID KAsymID L AsymID MAsymID N Biological Unit: protein homooctamer=4 copies of asymmetric unit

7. Unit PDB Un# # asym auth ent polymer polymertype source name asym 1jk9 0 1 A A 1 polymer polypeptide(L) pdb superoxide dismutase asym 1jk9 0 1 C C 1 polymer polypeptide(L) pdb superoxide dismutase asym 1jk9 0 1 B B 2 polymer polypeptide(L) pdb copper chaperone for superoxide dismutase asym 1jk9 0 1 D D 2 polymer polypeptide(L) pdb copper chaperone for superoxide dismutase asym 1jk9 0 1 E A 3 non-polymer - pdb ZINC ION asym 1jk9 0 1 F C 3 non-polymer - pdb ZINC ION asym 1jk9 0 1 G _ 3 non-polymer - pdb ZINC ION asym 1jk9 0 1 H _ 3 non-polymer - pdb ZINC ION asym 1jk9 0 1 I _ 4 non-polymer - pdb SULFATE ION asym 1jk9 0 1 J _ 4 non-polymer - pdb SULFATE ION asym 1jk9 0 1 K _ 5 water - pdb water rcsb 1jk9 1 1 A A 1 polymer polypeptide(L) pdb superoxide dismutase rcsb 1jk9 1 1 B B 2 polymer polypeptide(L) pdb copper chaperone for superoxide dismutase rcsb 1jk9 1 1 E A 3 non-polymer - pdb ZINC ION rcsb 1jk9 1 1 G _ 3 non-polymer - pdb ZINC ION rcsb 1jk9 1 1 H _ 3 non-polymer - pdb ZINC ION rcsb 1jk9 1 1 I _ 4 non-polymer - pdb SULFATE ION rcsb 1jk9 1 1 J _ 4 non-polymer - pdb SULFATE ION rcsb 1jk9 1 1 K _ 5 water - pdb water rcsb 1jk9 2 1 C C 1 polymer polypeptide(L) pdb superoxide dismutase rcsb 1jk9 2 1 D D 2 polymer polypeptide(L) pdb copper chaperone for superoxide dismutase rcsb 1jk9 2 1 F C 3 non-polymer - pdb ZINC ION pqs 1jk9 1 1 A A 1 polymer polypeptide(L) pdb superoxide dismutase pqs 1jk9 1 1 C C 1 polymer polypeptide(L) pdb superoxide dismutase pqs 1jk9 1 1 B B 2 polymer polypeptide(L) pdb copper chaperone for superoxide dismutase pqs 1jk9 1 1 D D 2 polymer polypeptide(L) pdb copper chaperone for superoxide dismutase pqs 1jk9 1 1 E A 3 non-polymer - pdb ZINC ION pqs 1jk9 1 1 F C 3 non-polymer - pdb ZINC ION pqs 1jk9 1 1 G _ 3 non-polymer - pdb ZINC ION pqs 1jk9 1 1 H _ 3 non-polymer - pdb ZINC ION pqs 1jk9 1 1 I _ 4 non-polymer - pdb SULFATE ION pqs 1jk9 1 1 J _ 4 non-polymer - pdb SULFATE ION pqs 1jk9 1 1 K _ 5 water - pdb water Content of Asymmetric and Biological Units