+Open data
-Basic information
Entry | Database: PDB / ID: 4al3 | ||||||
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Title | peptide deformylase (Co-form) with mercaptoethanol | ||||||
Components | PEPTIDE DEFORMYLASE | ||||||
Keywords | HYDROLASE / OXIDATION-REDUCTION | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Palm, G.J. / Hinrichs, W. | ||||||
Citation | Journal: Inorg.Chem. / Year: 2012 Title: A Fret Enzyme-Based Probe for Monitoring Hydrogen Sulfide. Authors: Strianese, M. / Palm, G.J. / Milione, S. / Kuhl, O. / Hinrichs, W. / Pellecchia, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4al3.cif.gz | 88.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4al3.ent.gz | 67 KB | Display | PDB format |
PDBx/mmJSON format | 4al3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/4al3 ftp://data.pdbj.org/pub/pdb/validation_reports/al/4al3 | HTTPS FTP |
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-Related structure data
Related structure data | 4al2C 4az4C 2w3tS 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: 21244.432 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: BL21(DE3) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P0A6K3, peptide deformylase |
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#2: Chemical | ChemComp-CO / |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-BME / |
#5: Water | ChemComp-HOH / |
Nonpolymer details | COBALT (II) ION (CO): REPLACES NATIVE DIVALENT FE BETA-MERCAPTOET |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.1 % Description: REFLECTIONS FROM 2.30 - 2.21 A REMOVED BECAUSE OF ICE RING |
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Crystal grow | Temperature: 293 K / pH: 6 Details: 20.5% PEG 4000, 100 MM NA-ACETATE PH 4.0, 293 K. TRANSFERRED TO 20% PEG, 50 MM ACETATE PH 6.0, THEN SOAKED WITH 10 MM MERCAPTOETHANOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 25, 2010 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→20 Å / Num. obs: 13528 / % possible obs: 88 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.98→2.09 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 6.3 / % possible all: 56 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2W3T Resolution: 1.98→48.18 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.896 / SU B: 15.129 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CO - BME S2 DISTANCE WAS RESTRAINED TO 2.30 ANGSTROM, ESD 0.10 A.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.616 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→48.18 Å
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Refine LS restraints |
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