+Open data
-Basic information
Entry | Database: PDB / ID: 8v5x | ||||||
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Title | UIC-1 mutant - UIC-1-L6A | ||||||
Components | UIC-1-L6A | ||||||
Keywords | DE NOVO PROTEIN / synthetic construct | ||||||
Function / homology | ACETONITRILE Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å | ||||||
Authors | Heinz-Kunert, S.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biomacromolecules / Year: 2024 Title: Pore Restructuring of Peptide Frameworks by Mutations at Distal Packing Residues. Authors: Heinz-Kunert, S.L. / Pandya, A. / Dang, V.T. / Oktawiec, J. / Nguyen, A.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8v5x.cif.gz | 32 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8v5x.ent.gz | 21.1 KB | Display | PDB format |
PDBx/mmJSON format | 8v5x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/8v5x ftp://data.pdbj.org/pub/pdb/validation_reports/v5/8v5x | HTTPS FTP |
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-Related structure data
Related structure data | 8v56C 8v59C 8v5wC 8v5zC 8v61C 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/peptide | Mass: 1332.509 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | #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: 1.57 Å3/Da / Density % sol: 21.58 % |
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Crystal grow | Temperature: 298 K / Method: slow cooling / Details: water, acetonitrile |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.61992 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 27, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.61992 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→17.55 Å / Num. obs: 6420 / % possible obs: 98.09 % / Redundancy: 6.3 % / Biso Wilson estimate: 9.06 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1191 / Rrim(I) all: 0.1304 / Net I/σ(I): 8.69 |
Reflection shell | Resolution: 1.12→1.16 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.7525 / Mean I/σ(I) obs: 2.55 / Num. unique obs: 593 / CC1/2: 0.734 / Rrim(I) all: 0.8301 / % possible all: 94.59 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.12→17.55 Å / SU ML: 0.1591 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 29.9154 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.67 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.12→17.55 Å
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Refine LS restraints |
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LS refinement shell |
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