+Open data
-Basic information
Entry | Database: PDB / ID: 7yh8 | |||||||||
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Title | Crystal structure of a heterochiral protein complex | |||||||||
Components |
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Keywords | DE NOVO PROTEIN / heterochiral / miniprotein / alpha helix / D-protein / D-peptide / mirror-image / de novo / designer | |||||||||
Function / homology | polypeptide(D) / polypeptide(D) (> 10) Function and homology information | |||||||||
Biological species | synthetic construct (others) artificial sequences (others) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Liang, M. / Li, S. / Wang, T. / Liu, L. / Lu, P. | |||||||||
Funding support | China, 2items
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Citation | Journal: Cell Res. / Year: 2024 Title: Accurate de novo design of heterochiral protein-protein interactions Authors: Sun, K. / Li, S. / Zheng, B. / Zhu, Y. / Wang, T. / Liang, M. / Yao, Y. / Zhang, K. / Zhang, J. / Li, H. / Han, D. / Zheng, J. / Coventry, B. / Cao, L. / Baker, D. / Liu, L. / Lu, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yh8.cif.gz | 50 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yh8.ent.gz | 35.4 KB | Display | PDB format |
PDBx/mmJSON format | 7yh8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yh8_validation.pdf.gz | 460.4 KB | Display | wwPDB validaton report |
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Full document | 7yh8_full_validation.pdf.gz | 462.7 KB | Display | |
Data in XML | 7yh8_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 7yh8_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yh/7yh8 ftp://data.pdbj.org/pub/pdb/validation_reports/yh/7yh8 | HTTPS FTP |
-Related structure data
Related structure data | 8gqpC 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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-Components
#1: Protein | Mass: 7303.665 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) #2: Polypeptide(D) | Mass: 2380.633 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: D amino acid / Source: (synth.) artificial sequences (others) #3: 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: 2.04 Å3/Da / Density % sol: 39.77 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% (W/V) PEG 8000, 100mM Tris base/Hydrochloric acid pH8.5, 100mM Magnesium chloride, 20% (V/V) PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 100K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Apr 23, 2022 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→50 Å / Num. obs: 8507 / % possible obs: 98.5 % / Redundancy: 4 % / Biso Wilson estimate: 28.78 Å2 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.028 / Rrim(I) all: 0.058 / Χ2: 0.952 / Net I/σ(I): 12.8 / Num. measured all: 34163 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→24.37 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.53 / Phase error: 27.85 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77 Å2 / Biso mean: 30.953 Å2 / Biso min: 15.63 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→24.37 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3
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