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Yorodumi- PDB-1v3y: The crystal structure of peptide deformylase from Thermus thermop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v3y | ||||||
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Title | The crystal structure of peptide deformylase from Thermus thermophilus HB8 | ||||||
Components | Peptide deformylase | ||||||
Keywords | HYDROLASE / peptide deformylase / protein synthesis / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information peptide deformylase / peptide deformylase activity / translation / metal ion binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | ||||||
Authors | Kamo, M. / Kudo, N. / Lee, W.C. / Ito, K. / Motoshim, H. / Tanokura, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: to be published Title: The crystal structure of peptide deformylase from Thermus thermophilus HB8 Authors: Kamo, M. / Kudo, N. / Lee, W.C. / Ito, K. / Motoshim, H. / Tanokura, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1v3y.cif.gz | 85.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v3y.ent.gz | 65.3 KB | Display | PDB format |
PDBx/mmJSON format | 1v3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1v3y_validation.pdf.gz | 439.3 KB | Display | wwPDB validaton report |
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Full document | 1v3y_full_validation.pdf.gz | 442.9 KB | Display | |
Data in XML | 1v3y_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 1v3y_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/1v3y ftp://data.pdbj.org/pub/pdb/validation_reports/v3/1v3y | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22171.316 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLys S / References: UniProt: P43522, peptide deformylase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 48.88 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% PEG 4000, 0.1M Tris-HCl, 200MM Sodium Acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 23, 2002 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→19.96 Å / Num. obs: 36563 / % possible obs: 99.4 % / Biso Wilson estimate: 34.4 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→19.8 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.059 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.116 / ESU R Free: 0.114 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.589 Å2
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Refinement step | Cycle: LAST / Resolution: 1.81→19.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.811→1.858 Å / Total num. of bins used: 20 /
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