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Open data
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Basic information
Entry | Database: PDB / ID: 2w3u | ||||||
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Title | formate complex of the Ni-Form of E.coli deformylase | ||||||
![]() | PEPTIDE DEFORMYLASE | ||||||
![]() | HYDROLASE / NICKEL / FORMATE COMPLEX | ||||||
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 | ![]() ![]() | ||||||
![]() | Ngo, Y.H.T. / Palm, G.J. / Hinrichs, W. | ||||||
![]() | ![]() Title: Structure of the Ni(II) Complex of Escherichia Coli Peptide Deformylase and Suggestions on Deformylase Activities Depending on Different Metal(II) Centres. Authors: Yen, N.T.H. / Bogdanovic, X. / Palm, G.J. / Kuhl, O. / Hinrichs, W. #1: ![]() Title: Iron Center, Substrate Recognition and Mechanism of Peptide Deformylase Authors: Becker, A. / Schlichting, I. / Kabsch, W. / Groche, D. / Schultz, S. / Wagner, A.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.5 KB | Display | ![]() |
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PDB format | ![]() | 35.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2w3tC ![]() 1xeoS 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: 21439.650 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-169 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NI / |
#3: Chemical | ChemComp-FMT / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.5 % / Description: NONE |
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Crystal grow | Temperature: 293 K / pH: 4.1 Details: 20% PEG4000, 0.2M (NH4)2SO4, 0.1M NAOAC PH 4.1, 293 K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU CCD / Detector: CCD / Date: Jun 24, 2007 / Details: OSMIC MULTILAYER |
Radiation | Monochromator: OSMIC MULTILAYER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→40 Å / Num. obs: 14750 / % possible obs: 95.5 % / Redundancy: 6.37 % / Biso Wilson estimate: 39.1 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.96→2.03 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.3 / % possible all: 64.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1XEO Resolution: 1.96→47.3 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.916 / SU B: 15.285 / SU ML: 0.185 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ONLY RESIDUAL U VALUES ARE SHOWN.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.223 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→47.3 Å
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Refine LS restraints |
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