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Yorodumi- PDB-1lm6: Crystal Structure of Peptide Deformylase from Streptococcus pneumoniae -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lm6 | ||||||
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Title | Crystal Structure of Peptide Deformylase from Streptococcus pneumoniae | ||||||
Components | peptide deformylase DEFB | ||||||
Keywords | HYDROLASE / PDF / Metalloenzyme / peptide deformylase | ||||||
Function / homology | Function and homology information peptide deformylase / peptide deformylase activity / translation / metal ion binding Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Kreusch, A. / Spraggon, G. / Lee, C.C. / Klock, H. / McMullan, D. / Ng, K. / Shin, T. / Vincent, J. / Warner, I. / Ericson, C. / Lesley, S.A. | ||||||
Citation | Journal: J.MOL.BIOL. / Year: 2003 Title: Structure analysis of peptide deformylases from streptococcus pneumoniae,staphylococcus aureus, thermotoga maritima, and pseudomonas aeruginosa: snapshots of the oxygen sensitivity of peptide deformylase Authors: Kreusch, A. / Spraggon, G. / Lee, C.C. / Klock, H. / McMullan, D. / Ng, K. / Shin, T. / Vincent, J. / Warner, I. / Ericson, C. / Lesley, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lm6.cif.gz | 56.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lm6.ent.gz | 39.2 KB | Display | PDB format |
PDBx/mmJSON format | 1lm6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lm6_validation.pdf.gz | 383.3 KB | Display | wwPDB validaton report |
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Full document | 1lm6_full_validation.pdf.gz | 385.6 KB | Display | |
Data in XML | 1lm6_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | 1lm6_validation.cif.gz | 9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lm/1lm6 ftp://data.pdbj.org/pub/pdb/validation_reports/lm/1lm6 | HTTPS FTP |
-Related structure data
Related structure data | 1lm4SC 1lmeC 1n5nC 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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Details | The biological unit is a monomer |
-Components
#1: Protein | Mass: 24230.684 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Plasmid: pMH1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9F2F0, peptide deformylase |
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#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | heterogen The modeled Fe(III) ion is a guess and has not been confirmed experimentally. |
Sequence details | THESE RESIDUES CORRESPOND TO THE FIRST SIX RESIDUES OF THIOREDOXIN FOLLOWED BY A HEXA-HIS ...THESE RESIDUES CORRESPOND |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.23 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG 8000, 0.2 M MgCl2, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 13, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→35 Å / Num. obs: 22277 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 8 % / Biso Wilson estimate: 22.7 Å2 / Rsym value: 0.048 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.75→1.85 Å / Num. unique all: 3661 / Rsym value: 0.241 / % possible all: 98.1 |
Reflection | *PLUS Lowest resolution: 50 Å / Rmerge(I) obs: 0.048 |
Reflection shell | *PLUS % possible obs: 98.1 % / Rmerge(I) obs: 0.241 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LM4 Resolution: 1.75→33.65 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2045273.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.1237 Å2 / ksol: 0.352357 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 29.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→33.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.207 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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