+Open data
-Basic information
Entry | Database: PDB / ID: 8zvh | ||||||
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Title | Crystal structure of AetD in complex with L-phenylalanine | ||||||
Components | AetD | ||||||
Keywords | METAL BINDING PROTEIN / nitrile synthase / iron-dependent / L-phenylalanine | ||||||
Function / homology | Haem oxygenase-like, multi-helical / metal ion binding / : / NICKEL (II) ION / PHENYLALANINE / AetD Function and homology information | ||||||
Biological species | Aetokthonos hydrillicola Thurmond2011 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | ||||||
Authors | Li, H. / Dai, L. / Zheng, H.B. / Chen, C.-C. / Guo, R.-T. | ||||||
Funding support | China, 1items
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Citation | Journal: Febs J. / Year: 2024 Title: Structural and molecular insights of two unique enzymes involved in the biosynthesis of a natural halogenated nitrile. Authors: Chen, C.C. / Li, H. / Huang, J.W. / Guo, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8zvh.cif.gz | 120.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8zvh.ent.gz | 91.4 KB | Display | PDB format |
PDBx/mmJSON format | 8zvh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8zvh_validation.pdf.gz | 3.8 MB | Display | wwPDB validaton report |
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Full document | 8zvh_full_validation.pdf.gz | 3.8 MB | Display | |
Data in XML | 8zvh_validation.xml.gz | 27.2 KB | Display | |
Data in CIF | 8zvh_validation.cif.gz | 37.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/8zvh ftp://data.pdbj.org/pub/pdb/validation_reports/zv/8zvh | HTTPS FTP |
-Related structure data
Related structure data | 8zvgC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28707.598 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aetokthonos hydrillicola Thurmond2011 (bacteria) Gene: aetD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A861B387 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NI / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.01 M nickel chloride, 20% PEG 2000 MME, 0.1 M Tris, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å |
Detector | Type: Bruker PHOTON III / Detector: PIXEL / Date: Aug 1, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.34138 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→32.54 Å / Num. obs: 39895 / % possible obs: 99.4 % / Redundancy: 6.3 % / CC1/2: 0.999 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.87→1.9 Å / Num. unique obs: 1866 / CC1/2: 0.831 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→32.54 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.381 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.162 / 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: 33.003 Å2
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Refinement step | Cycle: 1 / Resolution: 1.87→32.54 Å
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