+Open data
-Basic information
Entry | Database: PDB / ID: 1wlr | ||||||
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Title | Apo aminopeptidase P from E. coli | ||||||
Components | Xaa-Pro aminopeptidase | ||||||
Keywords | HYDROLASE / Proline-specific peptidase / metalloenzyme / pita-bread fold | ||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.1 Å | ||||||
Authors | Graham, S.C. / Bond, C.S. / Freeman, H.C. / Guss, J.M. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Structural and functional implications of metal ion selection in aminopeptidase p, a metalloprotease with a dinuclear metal center Authors: Graham, S.C. / Bond, C.S. / Freeman, H.C. / Guss, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wlr.cif.gz | 111.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wlr.ent.gz | 84.4 KB | Display | PDB format |
PDBx/mmJSON format | 1wlr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/1wlr ftp://data.pdbj.org/pub/pdb/validation_reports/wl/1wlr | HTTPS FTP |
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-Related structure data
Related structure data | 1w2mC 1w7vC 1wbqC 1wl6C 1wl9C 2bh3C 2bhaC 2bhbC 2bhcC 2bhdC 2bn7C C: citing same article (ref.) |
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Similar structure data |
-Links
-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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Details | The biological assembly is a homotetramer generated by the operators: (x,y,z), (1-x,1-y,z), (y,x,4/3-z), (1-y,1-x,4/3-z) |
-Components
#1: Protein | Mass: 49744.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pepP / Plasmid: pPL670 / Production host: Escherichia coli (E. coli) / Strain (production host): AN1459 / References: UniProt: P15034, Xaa-Pro aminopeptidase | ||
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#2: Chemical | ChemComp-CL / | ||
#3: Chemical | ChemComp-PG4 / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.4 Å3/Da / Density % sol: 72 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: TRIS, PEG 4000, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200H / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 8, 1998 / 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: 2.1→50 Å / Num. all: 47221 / Num. obs: 47221 / % possible obs: 90.2 % / Observed criterion σ(I): -3 / Net I/σ(I): 32.93 |
Reflection shell | Resolution: 2.1→2.18 Å / Num. unique all: 2200 / Rsym value: 0.0717 / % possible all: 59.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: Native aminopeptidase P without water, Mn or multiple conformers Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.571 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.815 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 64.777 Å / Origin y: 58.321 Å / Origin z: 49.668 Å
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