+Open data
-Basic information
Entry | Database: PDB / ID: 7vql | ||||||
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Title | de novo designed based on 1r26 | ||||||
Components | de novo designed protein | ||||||
Keywords | DE NOVO PROTEIN / de nove design protein | ||||||
Function / homology | AMMONIUM ION Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Zhang, L. | ||||||
Funding support | 1items
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Citation | Journal: Nat Comput Sci / Year: 2023 Title: Rotamer-free protein sequence design based on deep learning and self-consistency. Authors: Zhang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vql.cif.gz | 38 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vql.ent.gz | 23.9 KB | Display | PDB format |
PDBx/mmJSON format | 7vql.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/7vql ftp://data.pdbj.org/pub/pdb/validation_reports/vq/7vql | HTTPS FTP |
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-Related structure data
Related structure data | 7vqvC 7vqwC 7vtyC 7vu4C 1r26S 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: 12982.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) | ||||
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#2: Chemical | ChemComp-GOL / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.88 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate, BIS-Tris propane |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9875 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9875 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 14304 / % possible obs: 99.9 % / Redundancy: 12.1 % / CC1/2: 0.998 / Net I/σ(I): 38.41 |
Reflection shell | Resolution: 1.75→1.78 Å / Num. unique obs: 699 / CC1/2: 0.868 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1r26 Resolution: 1.75→34.58 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.815 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.124 / 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: 131.34 Å2 / Biso mean: 43.773 Å2 / Biso min: 23.42 Å2
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Refinement step | Cycle: final / Resolution: 1.75→34.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Rfactor Rfree error: 0
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