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Open data
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Basic information
Entry | Database: PDB / ID: 1m35 | ||||||
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Title | Aminopeptidase P from Escherichia coli | ||||||
![]() | AMINOPEPTIDASE P | ||||||
![]() | HYDROLASE / Aminopeptidase / proline specific / manganese enzyme | ||||||
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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Graham, S.C. / Lee, M. / Freeman, H.C. / Guss, J.M. | ||||||
![]() | ![]() Title: An orthorhombic form of Escherichia coli aminopeptidase P at 2.4 A resolution. Authors: Graham, S.C. / Lee, M. / Freeman, H.C. / Guss, J.M. #1: ![]() Title: Structure and mechanism of a proline-specific aminopeptidase from Escherichia coli Authors: Wilce, M.C.J. / Bond, C.S. / Dixon, N.E. / Freeman, H.C. / Guss, J.M. / Lilley, P.E. / Wilce, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 510.1 KB | Display | ![]() |
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PDB format | ![]() | 425.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.3 KB | Display | ![]() |
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Full document | ![]() | 490.5 KB | Display | |
Data in XML | ![]() | 106.2 KB | Display | |
Data in CIF | ![]() | 149.6 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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Unit cell |
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Details | Biological assembly is a tetramer formed by chains A,B,C and D / Biological assembly is a tetramer formed by chains E and F and the two-fold axis: x, -y, -z |
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Components
#1: Protein | Mass: 49744.062 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.58 Å3/Da / Density % sol: 72.92 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: PEG 4000, Tris.HCl, sodium acetate, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
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: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 25, 2002 Details: 58 cm long, Pt-coated, fused silica, vertical focus mirror |
Radiation | Monochromator: Cyclindrically bent triangular Si(111) asymmetric cut, horizontal focus monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. all: 197708 / Num. obs: 197708 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.16 % / Biso Wilson estimate: 34.7 Å2 / Limit h max: 87 / Limit h min: 0 / Limit k max: 130 / Limit k min: 0 / Limit l max: 67 / Limit l min: 0 / Observed criterion F max: 5063737.88 / Observed criterion F min: 17 / Rsym value: 0.058 / Net I/σ(I): 22.67 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.83 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 18004 / Rsym value: 0.3 / % possible all: 87.7 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.058 |
Reflection shell | *PLUS Lowest resolution: 2.51 Å / % possible obs: 87.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Tetramer of aminopeptidase P from Escherichia coli. Tetramer created from structure of hexagonal form (PDB code 1AZ9) using crystallographic symmetry ![]() 1az9 Resolution: 2.4→19.99 Å / Rfactor Rfree error: 0.002 / Occupancy max: 1 / Occupancy min: 1 Isotropic thermal model: Unrestrained, grouped. ARG, LYS, GLU and GLN had 3 groups per residue. Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 32.421 Å2 / ksol: 0.319566 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.49 Å2 / Biso mean: 37.91 Å2 / Biso min: 7.75 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.99 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: restrained / Weight Biso : 2 / Weight position: 100 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Lowest resolution: 2.51 Å |