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- PDB-5w3a: Crystal structure of mutant CJ YCEI protein (CJ-N182C) with 5-mer... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5w3a | ||||||
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Title | Crystal structure of mutant CJ YCEI protein (CJ-N182C) with 5-mercapto-2-nitrobenzoic acid guest structure | ||||||
![]() | Polyisoprenoid-binding protein | ||||||
![]() | UNKNOWN FUNCTION / nanotechnology / nanoporous | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Huber, T.R. / Snow, C.D. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 51.3 KB | Display | ![]() |
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PDB format | ![]() | 34.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 606.1 KB | Display | ![]() |
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Full document | ![]() | 607 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 11.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5w17C ![]() 5w2dC ![]() 5w2kC ![]() 5w2rC ![]() 5w2vC ![]() 5w2xC ![]() 5w2zC ![]() 5w30C ![]() 5w31C ![]() 5w32C ![]() 5w37SC ![]() 5w39C ![]() 5w3bC ![]() 5w3cC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20188.832 Da / Num. of mol.: 1 / Fragment: UNP residues 22-190 / Mutation: N182C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-LFA / | ||||
#3: Chemical | #4: Chemical | ChemComp-MNB / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.88 Å3/Da / Density % sol: 79.07 % / Mosaicity: 0.17 ° |
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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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 30, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.76→45.082 Å / Num. all: 12968 / Num. obs: 12968 / % possible obs: 100 % / Redundancy: 17.2 % / Rpim(I) all: 0.08 / Rrim(I) all: 0.337 / Rsym value: 0.327 / Net I/av σ(I): 2.3 / Net I/σ(I): 9 / Num. measured all: 222910 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 5W37 Resolution: 2.76→44.1 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.899 / SU B: 12.716 / SU ML: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.3 / ESU R Free: 0.258 / 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: 136.02 Å2 / Biso mean: 52.885 Å2 / Biso min: 20.93 Å2
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Refinement step | Cycle: final / Resolution: 2.76→44.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.76→2.831 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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