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- PDB-3b7i: Crystal structure of the S228A mutant of the aminopeptidase from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3b7i | ||||||
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Title | Crystal structure of the S228A mutant of the aminopeptidase from Vibrio proteolyticus in complex with leucine phosphonic acid | ||||||
![]() | Bacterial leucyl aminopeptidase | ||||||
![]() | HYDROLASE / alpha beta / Aminopeptidase / Metal-binding / Protease / Secreted / Zinc / Zymogen | ||||||
Function / homology | ![]() bacterial leucyl aminopeptidase / metalloexopeptidase activity / aminopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ataie, N.J. / Hoang, Q.Q. / Zahniser, M.P.D. / Milne, A. / Petsko, G.A. / Ringe, D. | ||||||
![]() | ![]() Title: Zinc coordination geometry and ligand binding affinity: the structural and kinetic analysis of the second-shell serine 228 residue and the methionine 180 residue of the aminopeptidase from Vibrio proteolyticus. Authors: Ataie, N.J. / Hoang, Q.Q. / Zahniser, M.P. / Tu, Y. / Milne, A. / Petsko, G.A. / Ringe, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.8 KB | Display | ![]() |
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PDB format | ![]() | 56.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3b35C ![]() 3b3cC ![]() 3b3sC ![]() 3b3tC ![]() 3b3vC ![]() 3b3wC ![]() 1ampS C: citing same article ( 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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Unit cell |
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Components on special symmetry positions |
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Details | Authors state that the biological unit of this protein is unknown. |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 31411.350 Da / Num. of mol.: 1 / Fragment: Residues 107-397 / Mutation: S228A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q01693, bacterial leucyl aminopeptidase |
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-Non-polymers , 7 types, 258 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SCN.gif)
![](data/chem/img/PLU.gif)
![](data/chem/img/LEU.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SCN.gif)
![](data/chem/img/PLU.gif)
![](data/chem/img/LEU.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-K / | #4: Chemical | #5: Chemical | ChemComp-SCN / | #6: Chemical | ChemComp-PLU / | #7: Chemical | ChemComp-LEU / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: HEPES, NaCl, KSCN, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9001 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→20.37 Å / Num. all: 32789 / Num. obs: 32789 / Observed criterion σ(I): 0 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1AMP Resolution: 1.75→20.37 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.042 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 mean: 14.089 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→20.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
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