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Yorodumi- PDB-4dr8: Crystal structure of a peptide deformylase from Synechococcus elo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dr8 | ||||||
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Title | Crystal structure of a peptide deformylase from Synechococcus elongatus | ||||||
Components | Peptide deformylase | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information peptide deformylase / peptide deformylase activity / translation / metal ion binding Similarity search - Function | ||||||
Biological species | Synechococcus elongatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Lorimer, D. / Abendroth, J. / Craig, T. / Burgin, A. / Segall, A. / Rohwer, F. | ||||||
Citation | Journal: ISME J / Year: 2013 Title: Structure and function of a cyanophage-encoded peptide deformylase. Authors: Frank, J.A. / Lorimer, D. / Youle, M. / Witte, P. / Craig, T. / Abendroth, J. / Rohwer, F. / Edwards, R.A. / Segall, A.M. / Burgin, A.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dr8.cif.gz | 313.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dr8.ent.gz | 256.5 KB | Display | PDB format |
PDBx/mmJSON format | 4dr8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/4dr8 ftp://data.pdbj.org/pub/pdb/validation_reports/dr/4dr8 | HTTPS FTP |
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-Related structure data
Related structure data | 3uwaC 3uwbC 4dr9C 1lryS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 21333.562 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC6301 / Gene: def, syc0213_d, YP_170923 / Plasmid: VCID 6622 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q5N5L5, UniProt: A0A0H3JZJ4*PLUS, peptide deformylase |
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-Non-polymers , 5 types, 992 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-FMT / #5: Chemical | ChemComp-CL / | #6: 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: 2.19 Å3/Da / Density % sol: 43.9 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: HAMPTON RESEARCH INDEX H12: 30% PEG 2000 MME, 150MM KBR, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127092 / Wavelength: 1.127092 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 31, 2012 |
Radiation | Monochromator: single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127092 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. all: 104822 / Num. obs: 99872 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.55→1.59 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 3.2 / Num. unique all: 7709 / Rsym value: 0.502 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb deposition 1lry Resolution: 1.55→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.74 / SU ML: 0.052 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.28 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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