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Yorodumi- PDB-7w5t: A nonheme iron- and alpha-ketoglutarate- dependent halogenase tha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7w5t | ||||||
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Title | A nonheme iron- and alpha-ketoglutarate- dependent halogenase that catalyzes nucleotide substrates | ||||||
Components | nonheme iron and alpha-ketoglutarate dependent halogenase | ||||||
Keywords | TRANSFERASE / halogenase | ||||||
Function / homology | Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / 2-OXOGLUTARIC ACID / : / DI(HYDROXYETHYL)ETHER / Isopenicillin N synthase-like Fe(2+) 2OG dioxygenase domain-containing protein Function and homology information | ||||||
Biological species | Actinomadura sp. ATCC 39365 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Dai, L.H. / Zhang, X. / Hu, Y.M. / Huang, J.W. / Chen, C.C. / Guo, R.T. | ||||||
Funding support | 1items
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Citation | Journal: Appl.Environ.Microbiol. / Year: 2022 Title: Structural and Functional Insights into a Nonheme Iron- and alpha-Ketoglutarate-Dependent Halogenase That Catalyzes Chlorination of Nucleotide Substrates. Authors: Dai, L. / Zhang, X. / Hu, Y. / Shen, J. / Zhang, Q. / Zhang, L. / Min, J. / Chen, C.C. / Liu, Y. / 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 | 7w5t.cif.gz | 81.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w5t.ent.gz | 56.1 KB | Display | PDB format |
PDBx/mmJSON format | 7w5t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/7w5t ftp://data.pdbj.org/pub/pdb/validation_reports/w5/7w5t | HTTPS FTP |
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-Related structure data
Related structure data | 7w5sSC 7w5vC S: Starting model for refinement 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34417.012 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Actinomadura sp. ATCC 39365 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1U8X168 |
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-Non-polymers , 6 types, 311 molecules
#2: Chemical | ChemComp-CL / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-AKG / | #5: Chemical | ChemComp-FE2 / | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
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: 2.25 Å3/Da / Density % sol: 45.27 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: Ammonium Sulfate, HEPES pH 7.5, PEG 400, di-Potassium hydrogen phosphate |
-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 100 / Detector: CMOS / Date: Dec 27, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.34138 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→32.71 Å / Num. obs: 32596 / % possible obs: 99.2 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.2 |
Reflection shell | Resolution: 1.74→1.77 Å / Rmerge(I) obs: 0.262 / Num. unique obs: 1599 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7W5S Resolution: 1.74→32.71 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.409 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.021 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 71.53 Å2 / Biso mean: 18.359 Å2 / Biso min: 1.06 Å2
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Refinement step | Cycle: final / Resolution: 1.74→32.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.74→1.785 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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