+Open data
-Basic information
Entry | Database: PDB / ID: 1kzq | ||||||
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Title | crystal structure of a parasite protein | ||||||
Components | Major Surface Antigen P30 | ||||||
Keywords | IMMUNE SYSTEM / SAG1 / major surface antigen / Toxoplasma Gondii / parasite invasion / MAD | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | He, X. / Grigg, M.E. / Boothroyd, J.C. / Garcia, K.C. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2002 Title: Structure of the immunodominant surface antigen from the Toxoplasma gondii SRS superfamily. Authors: He, X.L. / Grigg, M.E. / Boothroyd, J.C. / Garcia, K.C. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE AUTHORS HAVE FUNCTIONAL DATA SHOWING THE DIMER IS ACTIVE, AND BIOCHEMICAL DATA SHOWING A MIXTURE OF DIMER AND MONOMER IN SOLUTION. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kzq.cif.gz | 115.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kzq.ent.gz | 93.4 KB | Display | PDB format |
PDBx/mmJSON format | 1kzq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kzq_validation.pdf.gz | 436.7 KB | Display | wwPDB validaton report |
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Full document | 1kzq_full_validation.pdf.gz | 445.3 KB | Display | |
Data in XML | 1kzq_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 1kzq_validation.cif.gz | 42.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/1kzq ftp://data.pdbj.org/pub/pdb/validation_reports/kz/1kzq | 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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Unit cell |
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-Components
#1: Protein | Mass: 29829.877 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: SAG1 / Cell line (production host): High 5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P13664 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.87 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: Ammonium Sulfide, sodium acetate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.7→50 Å / Num. all: 72621 / Num. obs: 72621 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 7.5 | |||||||||||||||
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 10 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 1.9 / % possible all: 99.4 | |||||||||||||||
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 138104 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 99.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.7→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 31.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.8 Å / Rfactor Rfree error: 0.004 /
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Refinement | *PLUS Lowest resolution: 50 Å / Num. reflection obs: 138104 / % reflection Rfree: 5 % / Rfactor Rwork: 0.2 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 1.76 Å |