+Open data
-Basic information
Entry | Database: PDB / ID: 4az4 | ||||||
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Title | E.coli deformylase with Co(II) and hydrosulfide | ||||||
Components | PEPTIDE DEFORMYLASE | ||||||
Keywords | HYDROLASE / COBALT / HYDROGEN SULFIDE SENSOR | ||||||
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 / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 | 4az4.cif.gz | 86.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4az4.ent.gz | 65.6 KB | Display | PDB format |
PDBx/mmJSON format | 4az4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4az4_validation.pdf.gz | 428.9 KB | Display | wwPDB validaton report |
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Full document | 4az4_full_validation.pdf.gz | 429.1 KB | Display | |
Data in XML | 4az4_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 4az4_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/4az4 ftp://data.pdbj.org/pub/pdb/validation_reports/az/4az4 | HTTPS FTP |
-Related structure data
Related structure data | 4al2SC 4al3C 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 Details: C-TERMINAL HIS TAG / 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, UniProt: A0A140N556*PLUS, peptide deformylase |
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#2: Chemical | ChemComp-CO / |
#3: Chemical | ChemComp-H2S / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | COBALT (II) ION (CO): CO REPLACES THE NATIVE FE HYDROSULFURIC ACID (H2S): H2S IS BOUND AS ...COBALT (II) ION (CO): CO REPLACES THE NATIVE FE HYDROSULFU |
Sequence details | C-TERMINAL HIS TAG |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow | Temperature: 293 K / pH: 4.6 Details: 2 UL PROTEIN PLUS 2 UL (20% PEG 4000, 0.1 M NAOAC PH 4.6), 293 K. SOAKED IN 10% PEG4000, 20% PEG400, 0.1 M NAOAC PH 4.6, 293 K, FOR 1 DAY. INCUBATED IN H2S ATMOSPHERE EQUILIBRATED WITH 50 MM NA2S AT PH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 21, 2012 / Details: MIRRORS |
Radiation | Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 20010 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.1 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AL2 Resolution: 1.8→46.38 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.998 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 49.975 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→46.38 Å
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Refine LS restraints |
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