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Yorodumi- PDB-6ytj: Magnesium chelatase H subunit (ChlH) E625K variant from Synechocy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ytj | ||||||
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Title | Magnesium chelatase H subunit (ChlH) E625K variant from Synechocystis sp.PCC6803 | ||||||
Components | Mg-chelatase subunit ChlH | ||||||
Keywords | PHOTOSYNTHESIS / Magnesium chelatase / chlorophyll | ||||||
Function / homology | Function and homology information magnesium chelatase / magnesium chelatase activity / chlorophyll biosynthetic process / photosynthesis / ATP binding Similarity search - Function | ||||||
Biological species | Synechocystis sp. PCC 6803 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 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 | 6ytj.cif.gz | 511.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ytj.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6ytj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ytj_validation.pdf.gz | 450.6 KB | Display | wwPDB validaton report |
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Full document | 6ytj_full_validation.pdf.gz | 472.9 KB | Display | |
Data in XML | 6ytj_validation.xml.gz | 78.9 KB | Display | |
Data in CIF | 6ytj_validation.cif.gz | 107 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/6ytj ftp://data.pdbj.org/pub/pdb/validation_reports/yt/6ytj | HTTPS FTP |
-Related structure data
Related structure data | 6ys9C 6ysgSC 6yt0C 6ytnC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 150871.562 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-terminal His-tag and linker / Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: chlH / Production host: Escherichia coli (E. coli) / References: UniProt: P73020 #2: Water | ChemComp-HOH / | |
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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: 3.43 Å3/Da / Density % sol: 64.18 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.8-1.2 M sodium citrate and 2 mM dithiothreitol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→80.11 Å / Num. obs: 99929 / % possible obs: 100 % / Redundancy: 5.7 % / CC1/2: 0.993 / Rpim(I) all: 0.074 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.79→2.86 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 7451 / CC1/2: 0.583 / Rpim(I) all: 0.659 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6YSG Resolution: 2.79→80.105 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.9 / SU B: 17.004 / SU ML: 0.3 / Cross valid method: THROUGHOUT / ESU R: 0.643 / ESU R Free: 0.345 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.264 Å2
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Refinement step | Cycle: LAST / Resolution: 2.79→80.105 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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