+Open data
-Basic information
Entry | Database: PDB / ID: 1fc6 | ||||||
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Title | PHOTOSYSTEM II D1 C-TERMINAL PROCESSING PROTEASE | ||||||
Components | PHOTOSYSTEM II D1 PROTEASE | ||||||
Keywords | HYDROLASE / D1 C-terminal processing protease / serine protease / serine-lysine catalytic dyad / PDZ domain / photosystem II / photosynthesis / x-ray crystal structure | ||||||
Function / homology | Function and homology information C-terminal processing peptidase / chloroplast thylakoid lumen / serine-type endopeptidase activity / signal transduction / proteolysis Similarity search - Function | ||||||
Biological species | Scenedesmus obliquus (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD, treating MAD data as a special case of MIR / Resolution: 1.8 Å | ||||||
Authors | Liao, D.I. / Qian, J. / Chisholm, D.A. / Jordan, D.B. / Diner, B.A. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2000 Title: Crystal structures of the photosystem II D1 C-terminal processing protease. Authors: Liao, D.I. / Qian, J. / Chisholm, D.A. / Jordan, D.B. / Diner, B.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fc6.cif.gz | 88.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fc6.ent.gz | 69.8 KB | Display | PDB format |
PDBx/mmJSON format | 1fc6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fc6_validation.pdf.gz | 365.9 KB | Display | wwPDB validaton report |
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Full document | 1fc6_full_validation.pdf.gz | 378.3 KB | Display | |
Data in XML | 1fc6_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 1fc6_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/1fc6 ftp://data.pdbj.org/pub/pdb/validation_reports/fc/1fc6 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 41019.566 Da / Num. of mol.: 1 / Fragment: RESIDUES 77-464 / Mutation: L132M, L210M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Scenedesmus obliquus (plant) / Plasmid: PET-32(A)-D1P(+AM) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYS(MET-) / References: UniProt: O04073 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.86 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: PEG 4000, isopropanol, HEPES, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 102 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.9946 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 20, 1998 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9946 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 258532 / Num. obs: 35489 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.28 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.394 / Num. unique all: 1737 / % possible all: 99 |
Reflection | *PLUS Num. measured all: 258532 |
-Processing
Software |
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Refinement | Method to determine structure: MAD, treating MAD data as a special case of MIR Resolution: 1.8→30 Å / σ(F): 2 Stereochemistry target values: TNT library, Bond lengths 0.02 bond angles 3.00
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Solvent computation | Solvent model: Method implemented in the refinement program TNT Bsol: 248.14 Å2 / ksol: 0.86085 e/Å3 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.168 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_angle_deg / Dev ideal: 2.4 |