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Yorodumi- PDB-5w2r: Crystal structure of mutant CJ YCEI protein (CJ-G34C) with 5-merc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5w2r | ||||||
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Title | Crystal structure of mutant CJ YCEI protein (CJ-G34C) with 5-mercapto-2-nitrobenzoic acid guest structure | ||||||
Components | Polyisoprenoid-binding protein | ||||||
Keywords | UNKNOWN FUNCTION / nanotechnology nanoporous | ||||||
Function / homology | Function and homology information Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like superfamily / YceI-like domain / YceI-like domain / Lipocalin / Beta Barrel / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Campylobacter jejuni (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Huber, T.R. / Snow, C.D. | ||||||
Citation | Journal: Bioconjug. Chem. / Year: 2018 Title: Installing Guest Molecules at Specific Sites within Scaffold Protein Crystals. Authors: Huber, T.R. / McPherson, E.C. / Keating, C.E. / Snow, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5w2r.cif.gz | 50.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w2r.ent.gz | 34.5 KB | Display | PDB format |
PDBx/mmJSON format | 5w2r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5w2r_validation.pdf.gz | 459.8 KB | Display | wwPDB validaton report |
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Full document | 5w2r_full_validation.pdf.gz | 460.8 KB | Display | |
Data in XML | 5w2r_validation.xml.gz | 9 KB | Display | |
Data in CIF | 5w2r_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/5w2r ftp://data.pdbj.org/pub/pdb/validation_reports/w2/5w2r | HTTPS FTP |
-Related structure data
Related structure data | 5w17C 5w2dSC 5w2kC 5w2vC 5w2xC 5w2zC 5w30C 5w31C 5w32C 5w37C 5w39C 5w3aC 5w3bC 5w3cC C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 20245.883 Da / Num. of mol.: 1 / Mutation: G34C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: A0L11_08945, A0M64_02260, A0M70_03345, AD53_02580 / Plasmid: pSB3 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q79JB5, UniProt: Q0PB90*PLUS | ||||
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#2: Chemical | ChemComp-UNL / Mass: 282.547 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
#3: Chemical | #4: Chemical | ChemComp-MNB / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.7 Å3/Da / Density % sol: 78.44 % / Description: hexagonal |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 3.2 M Ammonium Sulfate, 0.1 M Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Apr 6, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→38.114 Å / Num. obs: 10917 / % possible obs: 99.7 % / Redundancy: 20.1 % / Rpim(I) all: 0.059 / Rrim(I) all: 0.262 / Rsym value: 0.255 / Net I/av σ(I): 2.3 / Net I/σ(I): 9.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5W2D Resolution: 2.9→38.114 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.92 / SU B: 17.195 / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.341 / ESU R Free: 0.295 / Details: 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 | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 212.15 Å2 / Biso mean: 99.483 Å2 / Biso min: 55.73 Å2
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Refinement step | Cycle: final / Resolution: 2.9→38.114 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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