+Open data
-Basic information
Entry | Database: PDB / ID: 1bsj | ||||||
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Title | COBALT DEFORMYLASE INHIBITOR COMPLEX FROM E.COLI | ||||||
Components | PROTEIN (PEPTIDE DEFORMYLASE) | ||||||
Keywords | HYDROLASE / DEFORMYLASE / INHIBITOR / METALLOPROTEINASE | ||||||
Function / homology | Function and homology information co-translational protein modification / peptide deformylase / peptide deformylase activity / ferrous iron binding / ribosome binding / hydrolase activity / translation / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Hao, B. / Gong, W. / Rajagopalan, P.T. / Hu, Y. / Pei, D. / Chan, M.K. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Structural basis for the design of antibiotics targeting peptide deformylase. Authors: Hao, B. / Gong, W. / Rajagopalan, P.T. / Zhou, Y. / Pei, D. / Chan, M.K. #1: Journal: Biochemistry / Year: 1997 Title: Crystal Structure of the Escherichia Coli Peptide Deformylase Authors: Chan, M.K. / Gong, W. / Rajagopalan, P.T. / Hao, B. / Tsai, C. / Pei, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bsj.cif.gz | 47.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bsj.ent.gz | 32.7 KB | Display | PDB format |
PDBx/mmJSON format | 1bsj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bsj_validation.pdf.gz | 452.6 KB | Display | wwPDB validaton report |
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Full document | 1bsj_full_validation.pdf.gz | 454.3 KB | Display | |
Data in XML | 1bsj_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 1bsj_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bs/1bsj ftp://data.pdbj.org/pub/pdb/validation_reports/bs/1bsj | HTTPS FTP |
-Related structure data
Related structure data | 1bskC 1dffS 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: 19226.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Cell line: BL21(DE3) / References: UniProt: P0A6K3, EC: 3.5.1.27 |
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#2: Chemical | ChemComp-CO / |
#3: Chemical | ChemComp-PO4 / |
#4: Chemical | ChemComp-MLN / ( |
#5: 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: 4.1 Å3/Da / Density % sol: 65 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: May 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 6591 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Rmerge(I) obs: 0.085 / Rsym value: 8.5 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.246 / Rsym value: 24.6 / % possible all: 97.3 |
Reflection | *PLUS Highest resolution: 2.1 Å / Num. obs: 16692 / % possible obs: 87.3 % / Num. measured all: 118933 / Rmerge(I) obs: 0.074 |
Reflection shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.19 Å / % possible obs: 87.7 % / Rmerge(I) obs: 0.236 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DFF Resolution: 3→20 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.14 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Num. reflection obs: 16692 / σ(F): 0 / % reflection Rfree: 8 % / Rfactor obs: 0.199 / Rfactor Rfree: 0.228 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 3 Å / Rfactor Rfree: 0.262 / % reflection Rfree: 7.3 % / Rfactor Rwork: 0.212 |