X-ray crystallography NMR Cryoelectron microscopy
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1 Molecular Graphics with PyMOL Overview of: Protein Data Bank Coordinates Jean-Yves Sgro PyMOL interface Hands-on! Experimental Methods 3 Main: X-ray crystallography NMR Cryoelectron microscopy X-ray source Bragg s law constructive Established 1971: 7 structures Tuesday May 23, 2017: 130,102 structures. destructive According to the 2θ deviation, the phase shift causes constructive or destructive interferences. September 27, 2016: 122,799 October 04, 2016: 123,021 February 07, 2017: 126,447
2 Exp.Method Proteins Nucleic Acids As of Tuesday May 3, 2017 Protein/NA Complexes Other Total Total % X-RAY % NMR % ELECTRON MICROSCOPY % HYBRID % other % Total % NMR 9% ELECTRON MICROSCOPY 1% Plain Text 80 columns Header 3D coordinates X-Ray 90% Connectivity End records HEADER CALCIUM-BINDING PROTEIN 08-OCT-93 1CDM 1CDM 2 COMPND CALMODULIN COMPLEXED WITH CALMODULIN-BINDING DOMAIN OF 1CDM 3 COMPND 2 CALMODULIN-DEPENDENT PROTEIN KINASE II 1CDM 4 SOURCE CALMODULIN: BOVINE (BOS TAURUS) BRAIN; PEPTIDE: SYNTHETIC 1CDM 5 SOURCE 2 BASED ON BOVINE (BOS TAURUS) BRAIN CALMODULIN-BINDING 1CDM 6 SOURCE 3 DOMAIN OF CALMODULIN-DEPENDENT PROTEIN KINASE 1CDM 7 AUTHOR W.E.MEADOR,F.A.QUIOCHO 1CDM 8 REVDAT 1 31-AUG-94 1CDM 0 1CDM 9 JRNL AUTH W.E.MEADOR,A.R.MEANS,F.A.QUIOCHO 1CDM 10 JRNL TITL MODULATION OF CALMODULIN PLASTICITY IN MOLECULAR 1CDM 11 JRNL TITL 2 RECOGNITION ON THE BASIS OF X-RAY STRUCTURES 1CDM 12 JRNL REF SCIENCE V CDM 13 JRNL REFN ASTM SCIEAS US ISSN CDM 14 SEQRES 1 A 144 LEU THR GLU GLU GLN ILE ALA GLU PHE LYS GLU ALA PHE 1CDM 52 SEQRES 2 A 144 SER LEU PHE ASP LYS ASP GLY ASP GLY THR ILE THR THR 1CDM 53 SEQRES 3 A 144 LYS GLU LEU GLY THR VAL MET ARG SER LEU GLY GLN ASN 1CDM 54 SEQRES 1 B 25 LEU LYS LYS PHE ASN ALA ARG ARG LYS LEU LYS GLY ALA 1CDM 64 SEQRES 2 B 25 ILE LEU THR THR MET LEU ALA THR ARG ASN PHE SER 1CDM 65 HET CA A 1 1 CALCIUM +2 COUN ION 1CDM 66 HET CA A 2 1 CALCIUM +2 COUN ION 1CDM 67 HET CA A 3 1 CALCIUM +2 COUN ION 1CDM 68 HET CA A 4 1 CALCIUM +2 COUN ION 1CDM 69 FORMUL 3 CA 4(CA1 ++) 1CDM 70 FORMUL 4 HOH *53(H2 O1) 1CDM 71 CRYST C CDM 72 ORIGX CDM 73 ORIGX CDM 74 ORIGX CDM 75 SCALE CDM 76 SCALE CDM 77 SCALE CDM 78 ATOM Serial # Atom Type Amino Acid Chain ID Sequence # X Y Z coordinates Occupancy (Scale Factor) Temperature Factor Optional ATOM 1 N LEU A CDM 79 ATOM 2 CA LEU A CDM 80 ATOM 3 C LEU A CDM 81 ATOM 4 O LEU A CDM 82 ATOM 5 CB LEU A CDM 83 ATOM 6 CG LEU A CDM 84 ATOM 7 CD1 LEU A CDM 85 ATOM 8 CD2 LEU A CDM 86 ATOM 9 N THR A CDM 87 ATOM 10 CA THR A CDM 88 ATOM 1037 O THR A CDM1115 ATOM 1038 CB THR A CDM1116 ATOM 1039 OG1 THR A CDM1117 ATOM 1040 CG2 THR A CDM1118 HETATM 1041 CA CA A CDM1119 HETATM 1042 CA CA A CDM1120 HETATM 1043 CA CA A CDM1121 HETATM 1044 CA CA A CDM1122 ATOM 1045 N PHE B CDM1123 ATOM 1046 CA PHE B CDM1124 ATOM 1047 C PHE B CDM1125 ATOM 1048 O PHE B CDM1126 ATOM 1049 CB PHE B CDM1127 ATOM 1050 CG PHE B CDM1128 ATOM 1051 CD1 PHE B CDM1129 ATOM 1052 CD2 PHE B CDM1130 ATOM 1053 CE1 PHE B CDM1131 René Descartes (Cartesius in Latin). The idea of this system was developed in 1637 in two writings by Descartes and independently by Pierre de Fermat, although Fermat used three dimensions and did not publish the discovery. (Ref: "analytic geometry". Encyclopædia Britannica (Encyclopædia Britannica Online ed.) )
3 Record Type MODEL & X Y Z coordinates ATOM 1181 CB THR B CDM1259 ATOM 1182 OG1 THR B CDM1260 ATOM 1183 CG2 THR B CDM THR B 310 1CDM1262 HETATM 1185 O HOH CDM1263 HETATM 1186 O HOH CDM1264 HETATM 1187 O HOH CDM1265 HETATM 1235 O HOH CDM1313 HETATM 1236 O HOH CDM1314 HETATM 1237 O HOH CDM1315 CONECT CDM1316 CONECT CDM1317 CONECT CDM1330 CONECT CDM1331 CONECT CDM1332 CONECT CDM1333 CONECT CDM1334 MAS CDM1335 END MODEL 1 ATOM 1 O5' G A O ATOM 2 C5' G A C ATOM 768 H6 C A H 769 C A 24 MODEL 2 ATOM 1 O5' G A O ATOM 2 C5' G A C / / MODEL 3 ATOM 1 O5' G A O ATOM 2 C5' G A C / / MODEL 1 ATOM LINES FOR CHAIN A ATOM LINES FOR CHAIN B MODEL 2 ATOM LINES FOR CHAIN A ATOM LINES FOR CHAIN B Header Connectivity End records 3D coordinates MODEL 1 3D coordinates MODEL 2 Example 1: 2biw APOCAROTENOID CLEAVAGE OXYGENASE Biological Unit 1 + Biological Unit 2 Asymmetric Unit Biological Unit 3 + Biological Unit 4 Example 2: 1DUD Escherichia coli dutpase in complex with a substrate analogue (dudp). Example 3: 1AYM HUMAN RHINOVIRUS 16 COAT PROTEIN AT HIGH RESOLUTION Asymmetric Unit x 3 = Assumed Biological Molecules REMARK 350 BIOMOLECULE: 1 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT REMARK 350 BIOMT REMARK 350 BIOMT REMARK 350 BIOMT REMARK 350 BIOMT REMARK 350 BIOMT REMARK 350 BIOMT REMARK 350 BIOMT REMARK 350 BIOMT Asymmetric Unit x 60 = Assumed Biological Molecules
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ame ection 7.014 Problem et 2 Answers to this problem set are to be turned in at the box outside 68120 by 4:00 pm Wednesday, February 20. Problem sets will not be accepted late. olutions will be posted
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