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Open data
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Basic information
Entry | Database: PDB / ID: 7q87 | ||||||
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Title | Carboxypeptidase T with (S)-3-phenyllactic acid | ||||||
![]() | Carboxypeptidase T | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() carboxypeptidase T / metallocarboxypeptidase activity / proteolysis / extracellular space / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Timofeev, V.I. / Akparov, V.K. / Shevtsov, M.B. / Kuranova, I.P. | ||||||
Funding support | 1items
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![]() | ![]() Title: Carboxypeptidase T with (S)-3-phenyllactic acid Authors: Timofeev, V.I. / Akparov, V.K. / Shevtsov, M.B. / Kuranova, I.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.4 KB | Display | ![]() |
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PDB format | ![]() | 68.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.4 KB | Display | ![]() |
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Full document | ![]() | 461.2 KB | Display | |
Data in XML | ![]() | 18.4 KB | Display | |
Data in CIF | ![]() | 28.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3qnvS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36641.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 376 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/HFA.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HFA.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: SA 1.4% |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7749 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→30 Å / Num. obs: 79136 / % possible obs: 99.98 % / Redundancy: 18.17 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 0.137 |
Reflection shell | Resolution: 1.73→1.82 Å / Rmerge(I) obs: 0.43 / Num. unique obs: 11382 / Rrim(I) all: 0.332 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3QNV Resolution: 1.73→29.94 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.915 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.052 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.31 Å2 / Biso mean: 15.146 Å2 / Biso min: 7.56 Å2
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Refinement step | Cycle: final / Resolution: 1.73→29.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.73→1.775 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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