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Yorodumi- PDB-5m2u: The Structure of the Ycf54 protein from Synechocystis sp. PCC6803 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m2u | |||||||||
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Title | The Structure of the Ycf54 protein from Synechocystis sp. PCC6803 | |||||||||
Components | Ycf54 | |||||||||
Keywords | PHOTOSYNTHESIS / Mg protoporphyrin IX monomethylester cyclase component. Ycf54 domain PFAM | |||||||||
Function / homology | Uncharacterised protein family Ycf54 / Ycf54 protein / Ycf54-like superfamily / Ycf54 protein / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / Ycf54-like protein Function and homology information | |||||||||
Biological species | Synechocystis sp. PCC 6803 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Baker, P.J. / Bliss, S. / Hollingshead, S. / Hunter, C.N. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Biochem. J. / Year: 2017 Title: Conserved residues in Ycf54 are required for protochlorophyllide formation in Synechocystis sp. PCC 6803. Authors: Hollingshead, S. / Bliss, S. / Baker, P.J. / Neil Hunter, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m2u.cif.gz | 99.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m2u.ent.gz | 76.2 KB | Display | PDB format |
PDBx/mmJSON format | 5m2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m2u_validation.pdf.gz | 444.5 KB | Display | wwPDB validaton report |
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Full document | 5m2u_full_validation.pdf.gz | 446.3 KB | Display | |
Data in XML | 5m2u_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 5m2u_validation.cif.gz | 25.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/5m2u ftp://data.pdbj.org/pub/pdb/validation_reports/m2/5m2u | HTTPS FTP |
-Related structure data
Related structure data | 5m2pSC 5m2rC 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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Unit cell |
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-Components
#1: Protein | Mass: 12392.982 Da / Num. of mol.: 4 / Mutation: R82A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: slr1780 / Production host: Escherichia coli (E. coli) / References: UniProt: P72777 #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: 3.05 Å3/Da / Density % sol: 59.66 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / Details: 2.2M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→27.8 Å / Num. obs: 31240 / % possible obs: 99.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 42.1 Å2 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.02 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2237 / Rpim(I) all: 0.35 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5M2P Resolution: 2.2→27.76 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.922 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.196 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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: 50.305 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→27.76 Å
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