+Open data
-Basic information
Entry | Database: PDB / ID: 6vlq | ||||||
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Title | Hop phytocystatin in space group P22121 | ||||||
Components | Hop1 | ||||||
Keywords | PROTEIN BINDING / cystatin / domain-swap / inhibitor / hop | ||||||
Biological species | Humulus lupulus (European hop) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.799 Å | ||||||
Authors | Valadares, F.F. / Moura, G.T. | ||||||
Funding support | Brazil, 1items
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Citation | Journal: Biochim Biophys Acta Proteins Proteom / Year: 2020 Title: Crystal structure and physicochemical characterization of a phytocystatin from Humulus lupulus: Insights into its domain-swapped dimer Authors: Moura, G.T. / Souza, A.A. / Garay, A.V. / Freitas, S.M. / Valadares, N.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vlq.cif.gz | 48.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vlq.ent.gz | 31.5 KB | Display | PDB format |
PDBx/mmJSON format | 6vlq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vlq_validation.pdf.gz | 260.6 KB | Display | wwPDB validaton report |
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Full document | 6vlq_full_validation.pdf.gz | 260.5 KB | Display | |
Data in XML | 6vlq_validation.xml.gz | 1 KB | Display | |
Data in CIF | 6vlq_validation.cif.gz | 1.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vl/6vlq ftp://data.pdbj.org/pub/pdb/validation_reports/vl/6vlq | HTTPS FTP |
-Related structure data
Related structure data | 6vlpC 4tx4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11258.755 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Humulus lupulus (European hop) / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo21 |
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#2: Chemical | ChemComp-SO4 / |
#3: 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: 1.6 Å3/Da / Density % sol: 23.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% w/v PEG8000, 100 mM sodium cacodylate, pH 6.5, 200 mM sodium acetate trihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 11, 2018 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.45 Å / Relative weight: 1 |
Reflection | Resolution: 1.799→25.78 Å / Num. obs: 6708 / % possible obs: 93.49 % / Redundancy: 2 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.01817 / Rrim(I) all: 0.02569 / Net I/σ(I): 18.35 |
Reflection shell | Resolution: 1.799→1.863 Å / Rmerge(I) obs: 0.8923 / Num. unique obs: 506 / CC1/2: 0.463 / CC star: 0.796 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4TX4 Resolution: 1.799→25.78 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 46.85 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.799→25.78 Å
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Refine LS restraints |
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