+Open data
-Basic information
Entry | Database: PDB / ID: 7nhe | ||||||
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Title | Crystal structure of Arabidopsis thaliana Pdx1K166R-I333 complex | ||||||
Components | Pyridoxal 5'-phosphate synthase subunit PDX1.3 | ||||||
Keywords | LYASE / VITAMIN B6 BIOSYTHESIS / PLP SYNTHASE / PDX1 | ||||||
Function / homology | Function and homology information response to non-ionic osmotic stress / response to lipid hydroperoxide / chlorophyll metabolic process / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / hyperosmotic salinity response / pyridoxal phosphate biosynthetic process / response to UV-B / amino acid metabolic process / endomembrane system ...response to non-ionic osmotic stress / response to lipid hydroperoxide / chlorophyll metabolic process / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / hyperosmotic salinity response / pyridoxal phosphate biosynthetic process / response to UV-B / amino acid metabolic process / endomembrane system / response to salt stress / response to oxidative stress / protein heterodimerization activity / protein homodimerization activity / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.23 Å | ||||||
Authors | Rodrigues, M.J. / Zhang, Y. / Bolton, R. / Evans, G. / Giri, N. / Royant, A. / Begley, T. / Ealick, S.E. / Tews, I. | ||||||
Citation | Journal: Rsc Chem Biol / Year: 2022 Title: Trapping and structural characterisation of a covalent intermediate in vitamin B 6 biosynthesis catalysed by the Pdx1 PLP synthase. Authors: Rodrigues, M.J. / Giri, N. / Royant, A. / Zhang, Y. / Bolton, R. / Evans, G. / Ealick, S.E. / Begley, T. / Tews, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nhe.cif.gz | 420.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nhe.ent.gz | 346.1 KB | Display | PDB format |
PDBx/mmJSON format | 7nhe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nh/7nhe ftp://data.pdbj.org/pub/pdb/validation_reports/nh/7nhe | HTTPS FTP |
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-Related structure data
Related structure data | 7nhfC 5lnuS 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 31210.072 Da / Num. of mol.: 4 / Mutation: K166R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PDX13, GIP2, PDX1L3, RSR4, At5g01410, T10O8.120 / Production host: Escherichia coli (E. coli) References: UniProt: Q8L940, pyridoxal 5'-phosphate synthase (glutamine hydrolysing) #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-KPR / [(~{ #4: 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: 2.82 Å3/Da / Density % sol: 56.45 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 28.1% PEG 1000 (w/v) and 100 mM HEPES pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.980023 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 17, 2013 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.980023 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.23→92.23 Å / Num. obs: 66508 / % possible obs: 99.7 % / Redundancy: 3.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.059 / Rrim(I) all: 0.12 / Net I/σ(I): 7.2 / Num. measured all: 260302 / Scaling rejects: 441 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5LNU Resolution: 2.23→92.23 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.94 / Phase error: 25.97 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 123.53 Å2 / Biso mean: 48.4446 Å2 / Biso min: 28.44 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.23→92.23 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24
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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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