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Yorodumi- PDB-8fhb: Protein 32 with aldehyde deformylating oxidase activity from Syne... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fhb | ||||||
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Title | Protein 32 with aldehyde deformylating oxidase activity from Synechococcus sp. | ||||||
Components | tRNA-(MS[2]IO[6]A)-hydroxylase | ||||||
Keywords | LYASE / aldehyde deformylating oxygenase | ||||||
Function / homology | tRNA-(2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine)-hydroxylase activity / tRNA-hydroxylase MiaE / tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE) / Ferritin-like / Ferritin-like superfamily / : / tRNA-(MS[2]IO[6]A)-hydroxylase Function and homology information | ||||||
Biological species | Synechococcus sp. RCC307 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å | ||||||
Authors | Arenas, R. / Wilson, D.K. / Mak, W.S. / Siegel, J.B. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Protein 32 with aldehyde deformylating oxidase activity from Synechococcus sp. Authors: Arenas, R. / Wilson, D.K. / Mak, W.S. / Siegel, J.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fhb.cif.gz | 60.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fhb.ent.gz | 39.3 KB | Display | PDB format |
PDBx/mmJSON format | 8fhb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fhb_validation.pdf.gz | 826.7 KB | Display | wwPDB validaton report |
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Full document | 8fhb_full_validation.pdf.gz | 827.1 KB | Display | |
Data in XML | 8fhb_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 8fhb_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/8fhb ftp://data.pdbj.org/pub/pdb/validation_reports/fh/8fhb | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25780.467 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus sp. RCC307 (bacteria) / Gene: miaE / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A5GR51 |
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#2: Chemical | ChemComp-FE / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 30% PEG 4,000, 200 mM MgCl2, 100 mM HEPES HCl |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→37.32 Å / Num. obs: 17168 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 27.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.017 / Rrim(I) all: 0.061 / Net I/σ(I): 26.7 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 1177 / CC1/2: 0.937 / Rpim(I) all: 0.186 / Rrim(I) all: 0.692 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.95→37.165 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.465 / SU ML: 0.098 / Cross valid method: FREE R-VALUE / ESU R: 0.142 / ESU R Free: 0.139 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.558 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→37.165 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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