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- PDB-3hm0: Crystal Structure of Probable Thioesterase from Bartonella henselae -
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Open data
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Basic information
Entry | Database: PDB / ID: 3hm0 | ||||||
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Title | Crystal Structure of Probable Thioesterase from Bartonella henselae | ||||||
![]() | Probable Thioesterase | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
![]() | ![]() Title: Crystal Structure of Probable Thioesterase from Bartonella henselae Authors: Edwards, T.E. / Staker, B.L. / Seattle Structural Genomics Center for Infectious Disease | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111.8 KB | Display | ![]() |
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PDB format | ![]() | 86.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2pzhS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19268.008 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.73 Å3/Da / Density % sol: 28.9 % |
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Crystal grow![]() | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Sparse matrix screen condition a9, 20% PEG 3350, 0.2 M ammonium chloride, 16 mg/mL protein, crystal tracking ID 202329a9, 0.1 mg/mL chymotrypsin, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 9, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.5→50 Å / Num. obs: 18932 / % possible obs: 99.4 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.121 / Χ2: 1.489 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 2.25 / Num. unique all: 1787 / Χ2: 1.287 / % possible all: 96.9 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2PZH Resolution: 2.5→40.01 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.898 / WRfactor Rfree: 0.248 / WRfactor Rwork: 0.194 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.792 / SU B: 10.882 / SU ML: 0.245 / SU R Cruickshank DPI: 0.84 / SU Rfree: 0.327 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.841 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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: 83.62 Å2 / Biso mean: 37.346 Å2 / Biso min: 11.62 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→40.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.566 Å / Total num. of bins used: 20
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