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Yorodumi- PDB-1bs4: PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM (NATIVE) IN COMPLEX W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bs4 | ||||||
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Title | PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM (NATIVE) IN COMPLEX WITH INHIBITOR POLYETHYLENE GLYCOL | ||||||
Components | PROTEIN (PEPTIDE DEFORMYLASE) | ||||||
Keywords | HYDROLASE / COMPLEX(ENZYME-INHIBITOR) / IRON METALLOPROTEASE / PROTEIN SYNTHESIS | ||||||
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: 1.9 Å | ||||||
Authors | Becker, A. / Schlichting, I. / Kabsch, W. / Groche, D. / Schultz, S. / Wagner, A.F.V. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1998 Title: Iron center, substrate recognition and mechanism of peptide deformylase. Authors: Becker, A. / Schlichting, I. / Kabsch, W. / Groche, D. / Schultz, S. / Wagner, A.F. #1: Journal: J.Biol.Chem. / Year: 1998 Title: Structure of Peptide Deformylase and Identification of the Substrate Binding Site Authors: Becker, A. / Schlichting, I. / Kabsch, W. / Schultz, S. / Wagner, A.F.V. #2: Journal: Biochem.Biophys.Res.Commun. / Year: 1998 Title: Isolation and Crystallization of Functionally Competent Escherichia Coli Peptide Deformylase Forms Containing Either Iron or Nickel in the Active Site Authors: Groche, D. / Becker, A. / Schlichting, I. / Kabsch, W. / Schultz, S. / Wagner, A.F.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bs4.cif.gz | 121.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bs4.ent.gz | 93.9 KB | Display | PDB format |
PDBx/mmJSON format | 1bs4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bs/1bs4 ftp://data.pdbj.org/pub/pdb/validation_reports/bs/1bs4 | HTTPS FTP |
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-Related structure data
Related structure data | 1bs5C 1bs6C 1bs8C 1bszC 1icjS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 19226.248 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: PDF PROTEIN FROM ESCHERICHIA COLI IS CRYSTALLIZED AS ZN2+ CONTAINING FORM, COCRYSTALLIZED WITH INHIBITOR POLYETHYLENE GLYCOL (PEG) Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM109 / Cellular location: CYTOPLASMA / Gene: DEF / Plasmid: P925C / Gene (production host): DEF / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P0A6K3, EC: 3.5.1.31 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.4 Details: REFERENCE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER ( 1998) BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: Groche, D., (1998) Biochem.Biophys.Res.Comm., 246, 342. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-18 / Wavelength: 1.5418 |
Detector | Type: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Jun 15, 1997 / Details: FRANKS DOUBLE-MIRROR |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 51676 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 16.63 |
Reflection shell | Resolution: 1.9→2.01 Å / Redundancy: 2 % / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 2.8 / % possible all: 98.4 |
Reflection | *PLUS Num. measured all: 188577 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ICJ Resolution: 1.9→6 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 28.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.01 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 6 Å / σ(F): 0 / % reflection Rfree: 10.1 % / Rfactor Rfree: 0.24 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 28.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.274 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.257 |