+Open data
-Basic information
Entry | Database: PDB / ID: 1prt | ||||||
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Title | THE CRYSTAL STRUCTURE OF PERTUSSIS TOXIN | ||||||
Components |
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Keywords | TOXIN | ||||||
Function / homology | Function and homology information NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / toxin activity / host cell plasma membrane / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Bordetella pertussis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.9 Å | ||||||
Authors | Stein, P.E. / Read, R.J. | ||||||
Citation | Journal: Structure / Year: 1994 Title: The crystal structure of pertussis toxin. Authors: Stein, P.E. / Boodhoo, A. / Armstrong, G.D. / Cockle, S.A. / Klein, M.H. / Read, R.J. | ||||||
History |
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Remark 700 | SHEET STRAND 2 OF SHEET *B1B* ALSO MAKES HYDROGEN BONDS WITH STRAND 2 OF SHEET *B3B*. LIKEWISE ...SHEET STRAND 2 OF SHEET *B1B* ALSO MAKES HYDROGEN BONDS WITH STRAND 2 OF SHEET *B3B*. LIKEWISE STRAND 2 OF SHEET *B1H* MAKES HYDROGEN BONDS WITH STRAND 2 OF SHEET *B3H*. STRAND 2 OF SHEET *B1C* ALSO MAKES HYDROGEN BONDS WITH STRAND 2 OF SHEET *B3C*. LIKEWISE STRAND 2 OF SHEET *B1I* MAKES HYDROGEN BONDS WITH STRAND 2 OF SHEET *B3I*. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1prt.cif.gz | 359 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1prt.ent.gz | 293 KB | Display | PDB format |
PDBx/mmJSON format | 1prt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1prt_validation.pdf.gz | 444.1 KB | Display | wwPDB validaton report |
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Full document | 1prt_full_validation.pdf.gz | 511.4 KB | Display | |
Data in XML | 1prt_validation.xml.gz | 44.2 KB | Display | |
Data in CIF | 1prt_validation.cif.gz | 66.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/1prt ftp://data.pdbj.org/pub/pdb/validation_reports/pr/1prt | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO A 196 / 2: CIS PROLINE - PRO D 84 / 3: CIS PROLINE - PRO E 84 / 4: CIS PROLINE - PRO G 196 / 5: CIS PROLINE - PRO J 84 / 6: CIS PROLINE - PRO K 84 | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9153, 0.3679, -0.163799), Vector: Details | EACH OF THE TWO HOLOTOXIN MOLECULES IN THE ASYMMETRIC UNIT CONSISTS OF SIX SUBUNITS AND THEY HAVE BEEN ASSIGNED CHAIN INDICATORS A - F AND G - L, RESPECTIVELY. SUBUNIT S1 OF EACH MOLECULE (CHAINS A AND G) FORMS THE ENZYMATIC PART OF THE TOXIN. THE REMAINING FIVE SUBUNITS S2, S3, TWO COPIES OF S4, AND S5 (CHAINS B - F AND H - L) FORM THE CELL-BINDING PART OF THE TOXIN. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS A - F WHEN APPLIED TO CHAINS G - L. | |
-Components
#1: Protein | Mass: 26133.652 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella pertussis (bacteria) / References: UniProt: P04977 #2: Protein | Mass: 21658.404 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella pertussis (bacteria) / References: UniProt: P04978 #3: Protein | Mass: 21622.543 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella pertussis (bacteria) / References: UniProt: P04979 #4: Protein | Mass: 12072.426 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella pertussis (bacteria) / References: UniProt: P0A3R5 #5: Protein | Mass: 10894.472 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella pertussis (bacteria) / References: UniProt: P04981 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.74 Å3/Da / Density % sol: 67.13 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Software |
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Refinement | Resolution: 2.9→10 Å / Rfactor Rwork: 0.195 / Rfactor obs: 0.195 / σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.195 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 1.8 |