+Open data
-Basic information
Entry | Database: PDB / ID: 7y10 | ||||||
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Title | Crystal structure of AtSFH5-Sec14 in complex with DPPA | ||||||
Components | Phosphatidylinositol/phosphatidylcholine transfer protein SFH5 | ||||||
Keywords | LIPID TRANSPORT / Sec14p homolog protein (SFH) / Arabidopsis thaliana / chloroplast / phosphatidic acid (PA) | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Lu, Y.Q. / Wang, X.Q. / Luo, Z.P. / Wu, J.W. | ||||||
Funding support | China, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2023 Title: Arabidopsis Sec14 proteins (SFH5 and SFH7) mediate interorganelle transport of phosphatidic acid and regulate chloroplast development. Authors: Yao, H.Y. / Lu, Y.Q. / Yang, X.L. / Wang, X.Q. / Luo, Z. / Lin, D.L. / Wu, J.W. / Xue, H.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y10.cif.gz | 140.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y10.ent.gz | 106.9 KB | Display | PDB format |
PDBx/mmJSON format | 7y10.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7y10_validation.pdf.gz | 834.8 KB | Display | wwPDB validaton report |
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Full document | 7y10_full_validation.pdf.gz | 842.4 KB | Display | |
Data in XML | 7y10_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | 7y10_validation.cif.gz | 38.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y1/7y10 ftp://data.pdbj.org/pub/pdb/validation_reports/y1/7y10 | HTTPS FTP |
-Related structure data
Related structure data | 7y11C 1auaS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 77 - 351 / Label seq-ID: 3 - 277
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-Components
#1: Protein | Mass: 34618.797 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: ...Details: MSLTIEDIHDVEELRAVDEFRNLLVSENLLPPTLDDYHIMLRFLKARKFDIGKTKLMWSNMIKWRKDFGTDTIFEDFEFEEFDEVLKYYPHGYHGVDKEGRPVYIERLGLVDPAKLMQVTTVERFIRYHVREFEKTVNIKLPACCIAAKRHIDSSTTILDVQGVGFKNFSKPARDLIIQLQKIDNDNYPETLHRMFIINGGSGFKLVWATVKQFLDPKTVTKIHVIGNKYQNKLLEIIDASQLPDFLGGTCTCADRGGCMRSDKGPWNDPEILKMLQSGGPLCRHNSALNSLEHHHHHH Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SFH5, At1g75370, F1B16.10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GXC6 #2: Chemical | #3: Chemical | ChemComp-NI / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.31 Å3/Da / Density % sol: 46.66 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES pH 6.0, 20% PEG6000, 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Mar 9, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 37354 / % possible obs: 99.2 % / Redundancy: 6.4 % / CC1/2: 0.991 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.067 / Rrim(I) all: 0.171 / Χ2: 1.123 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 5 % / Rmerge(I) obs: 0.837 / Mean I/σ(I) obs: 1.84 / Num. unique obs: 3480 / CC1/2: 0.525 / Rpim(I) all: 0.402 / Rrim(I) all: 0.933 / Χ2: 1.017 / % possible all: 93.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AUA Resolution: 2.1→21.44 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.917 / SU B: 6.096 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.278 / ESU R Free: 0.2 / 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: 146.85 Å2 / Biso mean: 33.322 Å2 / Biso min: 7.46 Å2
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Refinement step | Cycle: final / Resolution: 2.1→21.44 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 8839 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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