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Yorodumi- PDB-3n7t: Crystal structure of a macrophage binding protein from Coccidioid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n7t | ||||||
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Title | Crystal structure of a macrophage binding protein from Coccidioides immitis | ||||||
Components | Macrophage binding protein | ||||||
Keywords | PROTEIN BINDING / Seattle Structural Genomics Center for Infectious Disease / SSGCID / macrophage / pathogenic fungus / coccidioidomycosis / Valley Fever / meningitis | ||||||
Function / homology | DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / PHOSPHATE ION / Macrophage binding protein Function and homology information | ||||||
Biological species | Coccidioides immitis (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of a macrophage binding protein from Coccidioides immitis Authors: Edwards, T.E. / Abendroth, J. / Sankaran, B. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n7t.cif.gz | 111.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n7t.ent.gz | 84.4 KB | Display | PDB format |
PDBx/mmJSON format | 3n7t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3n7t_validation.pdf.gz | 446.8 KB | Display | wwPDB validaton report |
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Full document | 3n7t_full_validation.pdf.gz | 446.9 KB | Display | |
Data in XML | 3n7t_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 3n7t_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/3n7t ftp://data.pdbj.org/pub/pdb/validation_reports/n7/3n7t | HTTPS FTP |
-Related structure data
Related structure data | 1rw7 S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27191.564 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coccidioides immitis (fungus) / Gene: MBP-1 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HEU1 | ||||
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#2: Chemical | ChemComp-EDO / | ||||
#3: Chemical | #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.93 Å3/Da / Density % sol: 68.72 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 32.1 mg/mL protein against JCSG+ screen condition C6, 40% PEG 300, 0.1 M phosphate/citrate pH 4.2, crystal tracking ID 206576c6, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97946 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 21, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 25961 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 17.3 % / Biso Wilson estimate: 30.149 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 23.95 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 17.2 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 6.1 / Num. measured obs: 32014 / Num. unique obs: 1863 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 52.23 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1rw7 1rw7 Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.18 / WRfactor Rwork: 0.148 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.896 / SU B: 5.832 / SU ML: 0.071 / SU R Cruickshank DPI: 0.122 / SU Rfree: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.51 Å2 / Biso mean: 28.496 Å2 / Biso min: 14.49 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 38.355 Å / Origin y: 16.0546 Å / Origin z: 41.1014 Å
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