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Yorodumi- PDB-1xrm: Crystal structure of active site F1-mutant E213Q soaked with pept... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xrm | ||||||
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Title | Crystal structure of active site F1-mutant E213Q soaked with peptide Ala-Phe | ||||||
Components | Proline iminopeptidase | ||||||
Keywords | HYDROLASE / ALPHA-BETA HYDROLASE / CAGED ACTIVE SITE / SUBSTRATE RECOGNITION / HYDROGEN BONDED NETWORK / PEPTIDE CLEAVAGE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermoplasma acidophilum (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Goettig, P. / Brandstetter, H. / Groll, M. / Goehring, W. / Konarev, P.V. / Svergun, D.I. / Huber, R. / Kim, J.-S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: X-ray snapshots of peptide processing in mutants of tricorn-interacting factor F1 from Thermoplasma acidophilum Authors: Goettig, P. / Brandstetter, H. / Groll, M. / Goehring, W. / Konarev, P.V. / Svergun, D.I. / Huber, R. / Kim, J.-S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xrm.cif.gz | 72.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xrm.ent.gz | 53.1 KB | Display | PDB format |
PDBx/mmJSON format | 1xrm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xr/1xrm ftp://data.pdbj.org/pub/pdb/validation_reports/xr/1xrm | HTTPS FTP |
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-Related structure data
Related structure data | 1xqvC 1xqwC 1xqxC 1xqyC 1xrlC 1xrnC 1xroC 1xrpC 1xrqC 1xrrC 1mtzS S: Starting model for refinement 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
#1: Protein | Mass: 33529.105 Da / Num. of mol.: 1 / Mutation: E213Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: TA0830 / Plasmid: PRSET6C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P96084, prolyl aminopeptidase | ||||
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#2: Chemical | #3: Chemical | ChemComp-ALA / | #4: 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: 2.15 Å3/Da / Density % sol: 42.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 6000, Bis-Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 2003 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→19 Å / Num. all: 7647 / Num. obs: 7564 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 73.1 Å2 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.7→2.87 Å / % possible all: 60.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MTZ Resolution: 2.7→16.71 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 1005675.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.9449 Å2 / ksol: 0.459151 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→16.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.062 / Total num. of bins used: 6
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Xplor file |
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