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Open data
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Basic information
Entry | Database: PDB / ID: 1n51 | |||||||||
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Title | Aminopeptidase P in complex with the inhibitor apstatin | |||||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / AMINOPEPTIDASE / PROLINE SPECIFIC / MANGANESE ENZYME / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | |||||||||
Function / homology | ![]() Xaa-Pro aminopeptidase / metalloexopeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / manganese ion binding / protein homotetramerization / protein-containing complex / proteolysis / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() synthetic (others) | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Graham, S.C. / Maher, M.J. / Lee, M.H. / Simmons, W.H. / Freeman, H.C. / Guss, J.M. | |||||||||
![]() | ![]() Title: Structure of Escherichia coli aminopeptidase P in complex with the inhibitor apstatin. Authors: Graham, S.C. / Maher, M.J. / Simmons, W.H. / Freeman, H.C. / Guss, J.M. #1: ![]() Title: Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination Authors: Brunger, A.T. / Adams, P.D. / Clore, G.M. / Delano, W.L. / Gros, P. / Grosse-Kunstleve, R. / Jiang, J.-S. / Kuszewski, J. / Nilges, M. / Pannu, N.S. / Read, R.J. / Rice, L.M. / Simonson, T. / Warren, G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113 KB | Display | ![]() |
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PDB format | ![]() | 85.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.4 KB | Display | ![]() |
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Full document | ![]() | 440.3 KB | Display | |
Data in XML | ![]() | 22.1 KB | Display | |
Data in CIF | ![]() | 33.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1az9 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | Biological assembly is a tetramer formed by the crystallographic operations: (X,Y,Z), (-Y+1/2,-X+1/2,-Z+1/2), (Y-1/2,X+1/2,-Z+1/2), (-X,1-Y,Z) |
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Components
#1: Protein | Mass: 49744.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Protein/peptide | | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.02 Å3/Da / Density % sol: 75.28 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: Magnesium Acetate, Sodium Cacodylate, MPD, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 24, 2000 / Details: YALE MIRRORS |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→99 Å / Num. all: 48993 / Num. obs: 55327 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 42.6 Å2 / Limit h max: 63 / Limit h min: 0 / Limit k max: 44 / Limit k min: 0 / Limit l max: 104 / Limit l min: 0 / Observed criterion F max: 3136609.46 / Observed criterion F min: 17.3 / Rmerge(I) obs: 0.046 / Net I/σ(I): 16.58 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 1.83 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 1.46 / Num. unique all: 4729 / % possible all: 83.1 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 20 Å / % possible obs: 97 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.044 |
Reflection shell | *PLUS % possible obs: 96.2 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB 1AZ9 ![]() 1az9 Resolution: 2.3→19.9 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 37.434 Å2 / ksol: 0.299544 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.3 Å2 / Biso mean: 44.58 Å2 / Biso min: 18.16 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→19.9 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.333 / Rfactor Rwork: 0.299 / Num. reflection Rwork: 5361 |