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Yorodumi- PDB-6ys9: T_926 truncate of ChlH from Thermosynechococcus elongatus at 1.64... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ys9 | ||||||
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Title | T_926 truncate of ChlH from Thermosynechococcus elongatus at 1.64 A resolution | ||||||
Components | Magnesium-protoporphyrin methyltransferase | ||||||
Keywords | PHOTOSYNTHESIS / Magnesium chelatase / chlorophyll / bacteriochlorophyll | ||||||
Function / homology | Function and homology information magnesium chelatase / magnesium chelatase activity / chlorophyll biosynthetic process / photosynthesis / methyltransferase activity / methylation / ATP binding Similarity search - Function | ||||||
Biological species | Thermosynechococcus elongatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | ||||||
Authors | Bisson, C. / Hunter, C.N. | ||||||
Funding support | 1items
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Citation | Journal: Nat.Plants / Year: 2020 Title: The active site of magnesium chelatase. Authors: Adams, N.B.P. / Bisson, C. / Brindley, A.A. / Farmer, D.A. / Davison, P.A. / Reid, J.D. / Hunter, C.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ys9.cif.gz | 309 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ys9.ent.gz | 259.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ys9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ys/6ys9 ftp://data.pdbj.org/pub/pdb/validation_reports/ys/6ys9 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 46093.746 Da / Num. of mol.: 4 / Mutation: Truncated at the N-terminus Source method: isolated from a genetically manipulated source Details: C-terminal His-tag Source: (gene. exp.) Thermosynechococcus elongatus (strain BP-1) (bacteria) Gene: chlH / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DM52 #2: Chemical | ChemComp-K / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.15 Å3/Da / Density % sol: 42.82 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20-22% PEG 6000, 100 mM Tris pH 8, 200 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97633 Å | |||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 8, 2015 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97633 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.64→64.38 Å / Num. obs: 172739 / % possible obs: 91.2 % / Redundancy: 2.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.057 / Rrim(I) all: 0.093 / Net I/σ(I): 7.4 | |||||||||||||||
Reflection shell | Resolution: 1.64→1.68 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.544 / Num. unique obs: 10643 / CC1/2: 0.487 / Rpim(I) all: 0.442 / Rrim(I) all: 0.704 / % possible all: 76.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SeMet poly-Ala model Resolution: 1.64→64.38 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / SU B: 1.91 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.024 / ESU R Free: 0.025 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 200 Å2 / Biso mean: 24.569 Å2 / Biso min: 2.32 Å2
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Refinement step | Cycle: final / Resolution: 1.64→64.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.611→1.653 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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