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Yorodumi- PDB-1lme: Crystal Structure of Peptide Deformylase from Thermotoga maritima -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lme | ||||||
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Title | Crystal Structure of Peptide Deformylase from Thermotoga maritima | ||||||
Components | peptide deformylase | ||||||
Keywords | HYDROLASE / thermophile / PDF / peptide deformylase / metalloenzyme / deformylation / Structural Genomics / PSI / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG | ||||||
Function / homology | Function and homology information co-translational protein modification / N-terminal protein amino acid modification / peptidyl-methionine modification / peptide deformylase / peptide deformylase activity / translation / metal ion binding Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Kreusch, A. / Spraggon, G. / Lee, C.C. / Klock, H. / McMullan, D. / Ng, K. / Shin, T. / Vincent, J. / Warner, I. / Ericson, C. ...Kreusch, A. / Spraggon, G. / Lee, C.C. / Klock, H. / McMullan, D. / Ng, K. / Shin, T. / Vincent, J. / Warner, I. / Ericson, C. / Lesley, S.A. / Joint Center for Structural Genomics (JCSG) | ||||||
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 | 1lme.cif.gz | 75.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lme.ent.gz | 56.2 KB | Display | PDB format |
PDBx/mmJSON format | 1lme.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lme_validation.pdf.gz | 383.1 KB | Display | wwPDB validaton report |
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Full document | 1lme_full_validation.pdf.gz | 386.8 KB | Display | |
Data in XML | 1lme_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 1lme_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lm/1lme ftp://data.pdbj.org/pub/pdb/validation_reports/lm/1lme | HTTPS FTP |
-Related structure data
Related structure data | 1lm4C 1lm6C 1n5nC 1bs4S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20563.771 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: pMH1 / Production host: Escherichia coli (E. coli) / References: UniProt: P96113, 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: 2.25 Å3/Da / Density % sol: 45.26 % | ||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: PEG 3350, potassium nitrate, pH 6.9, 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: Jan 8, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→45.2 Å / Num. obs: 19503 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 27.7 Å2 / Rsym value: 0.075 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.2→2.34 Å / Num. unique all: 3137 / Rsym value: 0.327 / % possible all: 98.9 |
Reflection | *PLUS Lowest resolution: 50 Å / % possible obs: 99.6 % / Rmerge(I) obs: 0.075 |
Reflection shell | *PLUS % possible obs: 98.8 % / Rmerge(I) obs: 0.327 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BS4 Resolution: 2.2→45.19 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 29.2696 Å2 / ksol: 0.379437 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 27.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→45.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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