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Open data
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Basic information
Entry | Database: PDB / ID: 1bs5 | ||||||
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Title | PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM | ||||||
![]() | PROTEIN (PEPTIDE DEFORMYLASE) | ||||||
![]() | HYDROLASE / IRON METALLOPROTEASE / PROTEIN SYNTHESIS | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Becker, A. / Schlichting, I. / Kabsch, W. / Groche, D. / Schultz, S. / Wagner, A.F.V. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 114.4 KB | Display | ![]() |
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PDB format | ![]() | 88 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.1 KB | Display | ![]() |
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Full document | ![]() | 467.3 KB | Display | |
Data in XML | ![]() | 21.7 KB | Display | |
Data in CIF | ![]() | 29.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1bs4C ![]() 1bs6C ![]() 1bs8C ![]() 1bszC ![]() 1icjS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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 Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.4 Details: SEE: 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: ![]() |
Detector | Type: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Jul 15, 1997 / Details: FRANCKS DUBBLE-MIRROR OPTICS |
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: 2.5→20 Å / Num. obs: 22399 / % possible obs: 99.3 % / Redundancy: 5.8 % / Biso Wilson estimate: 43.6 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 15.72 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 1.9 / % possible all: 99.4 |
Reflection | *PLUS Num. measured all: 130772 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ICJ Resolution: 2.5→6 Å / Rfactor Rfree error: 0.006 / 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: 37 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.64 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 6 Å / σ(F): 0 / % reflection Rfree: 10.4 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 37 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.349 / % reflection Rfree: 9.2 % / Rfactor Rwork: 0.294 |