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- PDB-6ysg: Magnesium chelatase H subunit (ChlH) from Synechocystis sp.PCC680... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ysg | ||||||
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Title | Magnesium chelatase H subunit (ChlH) from Synechocystis sp.PCC6803 to 2.54 A resolution | ||||||
![]() | Mg-chelatase subunit ChlH | ||||||
![]() | PHOTOSYNTHESIS / Magnesium chelatase / chlorophyll | ||||||
Function / homology | ![]() magnesium chelatase / magnesium chelatase activity / chlorophyll biosynthetic process / photosynthesis / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bisson, C. / Hunter, C.N. | ||||||
Funding support | 1items
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 501.6 KB | Display | ![]() |
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PDB format | ![]() | 399.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 469.3 KB | Display | ![]() |
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Full document | ![]() | 493.2 KB | Display | |
Data in XML | ![]() | 81.7 KB | Display | |
Data in CIF | ![]() | 112.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ys9C ![]() 6yt0C ![]() 6ytjC ![]() 6ytnC ![]() 4zhjS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 150871.500 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-terminal His-tag Source: (gene. exp.) ![]() ![]() Gene: chlH / Production host: ![]() ![]() #2: Chemical | ChemComp-CIT / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.37 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.8-1.2M Sodium citrate pH7.0 and 2 mM dithiothreitol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2015 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98674 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.54→83.78 Å / Num. obs: 133090 / % possible obs: 100 % / Redundancy: 8.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.041 / Rrim(I) all: 0.12 / Net I/σ(I): 12.1 / Num. measured all: 1143007 / Scaling rejects: 509 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ZHJ Resolution: 2.54→83.78 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.92 / SU B: 11.297 / SU ML: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.338 / ESU R Free: 0.261 / 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: 177.89 Å2 / Biso mean: 58.372 Å2 / Biso min: 22.51 Å2
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Refinement step | Cycle: final / Resolution: 2.54→83.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.54→2.606 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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