+Open data
-Basic information
Entry | Database: PDB / ID: 7yth | ||||||
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Title | Structure of OCPx1 from Nostoc flagelliforme CCNUN1 | ||||||
Components | Ketosteroid isomerase-related protein | ||||||
Keywords | PHOTOSYNTHESIS / OCP protein | ||||||
Function / homology | Function and homology information light absorption / phycobilisome / chloride ion binding / isomerase activity Similarity search - Function | ||||||
Biological species | Nostoc flagelliforme CCNUN1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Yang, Y.W. / Liu, K. / Chen, S.Z. / Chen, M. / Qiu, B.S. | ||||||
Funding support | China, 1items
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Citation | Journal: Plant Physiol. / Year: 2023 Title: Functional specialization of expanded orange carotenoid protein paralogs in subaerial Nostoc species. Authors: Yang, Y.W. / Liu, K. / Huang, D. / Yu, C. / Chen, S.Z. / Chen, M. / Qiu, B.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yth.cif.gz | 259.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yth.ent.gz | 209.2 KB | Display | PDB format |
PDBx/mmJSON format | 7yth.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yth_validation.pdf.gz | 460.4 KB | Display | wwPDB validaton report |
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Full document | 7yth_full_validation.pdf.gz | 474.6 KB | Display | |
Data in XML | 7yth_validation.xml.gz | 49 KB | Display | |
Data in CIF | 7yth_validation.cif.gz | 70.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/7yth ftp://data.pdbj.org/pub/pdb/validation_reports/yt/7yth | HTTPS FTP |
-Related structure data
Related structure data | 7ytfC 4xb5S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35943.094 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc flagelliforme CCNUN1 (bacteria) / Gene: COO91_01637 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2K8SJT8 #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: 2.48 Å3/Da / Density % sol: 50.39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97935 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→79.78 Å / Num. obs: 103819 / % possible obs: 98.7 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.93→1.98 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 7107 / CC1/2: 0.854 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XB5 Resolution: 1.93→67.01 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.536 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.158 / 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: 128.06 Å2 / Biso mean: 45.511 Å2 / Biso min: 25.38 Å2
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Refinement step | Cycle: final / Resolution: 1.93→67.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→1.978 Å / Rfactor Rfree error: 0
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