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Yorodumi- PDB-4xae: Structure of Feruloyl-CoA 6-hydroxylase (F6H) from Arabidopsis th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xae | ||||||
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Title | Structure of Feruloyl-CoA 6-hydroxylase (F6H) from Arabidopsis thaliana | ||||||
Components | Feruloyl CoA ortho-hydroxylase 1 | ||||||
Keywords | OXIDOREDUCTASE / PROTEIN ENGINEERING / COUMARINS / 2-oxoglutarate dependent dioxygenase | ||||||
Function / homology | Function and homology information feruloyl-CoA 6-hydroxylase / hydrogen peroxide-mediated programmed cell death / response to iron ion starvation / coumarin biosynthetic process / phenylpropanoid biosynthetic process / dioxygenase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.769 Å | ||||||
Authors | Zhou, D. / Kandavelu, P. / Zhang, H. / Wang, B.C. / Rose, J. / Yan, Y. | ||||||
Citation | Journal: Sci Rep / Year: 2015 Title: Structural Insights into Substrate Specificity of Feruloyl-CoA 6'-Hydroxylase from Arabidopsis thaliana. Authors: Sun, X. / Zhou, D. / Kandavelu, P. / Zhang, H. / Yuan, Q. / Wang, B.C. / Rose, J. / Yan, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xae.cif.gz | 267.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xae.ent.gz | 216.4 KB | Display | PDB format |
PDBx/mmJSON format | 4xae.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xae_validation.pdf.gz | 445.1 KB | Display | wwPDB validaton report |
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Full document | 4xae_full_validation.pdf.gz | 454.4 KB | Display | |
Data in XML | 4xae_validation.xml.gz | 24.9 KB | Display | |
Data in CIF | 4xae_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/4xae ftp://data.pdbj.org/pub/pdb/validation_reports/xa/4xae | HTTPS FTP |
-Related structure data
Related structure data | 1gp4S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 42306.938 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: F6'H1, At3g13610, K20M4.5 / Production host: Escherichia coli (E. coli) References: UniProt: Q9LHN8, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.13 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Sitting drop vapor diffusion at 291K using 2 microliter drops containing equal volumes of protein concentrate and a precipitant cocktail containing 20% (w/v) PEG-8000, 0.1 M MES, 0.3 M Ca(OAc)2, pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 30, 2014 |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→44.93 Å / Num. all: 19697 / Num. obs: 19697 / % possible obs: 92.21 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.7→2.795 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 2.01 / % possible all: 59.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GP4 Resolution: 2.769→44.93 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.38 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.769→44.93 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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