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- PDB-8hjx: Crystal structure of a cupin protein (tm1459, H52A/H58E mutant) i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hjx | |||||||||
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Title | Crystal structure of a cupin protein (tm1459, H52A/H58E mutant) in copper (Cu) substituted form | |||||||||
![]() | Cupin_2 domain-containing protein | |||||||||
![]() | METAL BINDING PROTEIN / Artificial metalloenzymes / Non-heme copper enzyme / Cupin | |||||||||
Function / homology | Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / metal ion binding / COPPER (II) ION / Cupin type-2 domain-containing protein![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Matsumoto, R. / Kurisu, G. / Fujieda, N. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: An artificial metallolyase with pliable 2-His-1-carboxylate facial triad for stereoselective Michael addition. Authors: Matsumoto, R. / Yoshioka, S. / Yuasa, M. / Morita, Y. / Kurisu, G. / Fujieda, N. #1: ![]() Title: An artificial metallolyase with pliable 2-His-1-carboxylate facial triad for stereoselective Michael addition. Authors: Matsumoto, R. / Yoshioka, S. / Yuasa, M. / Morita, Y. / Kurisu, G. / Fujieda, N. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 159.1 KB | Display | ![]() |
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PDB format | ![]() | 129.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.2 KB | Display | ![]() |
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Full document | ![]() | 431.2 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 20.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hjyC ![]() 8hjzC ![]() 6l2eS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 13383.267 Da / Num. of mol.: 2 / Mutation: H52A/H58E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% w/v Jeffamine ED-2001, 0.1M MES pH6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 16, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→99 Å / Num. obs: 151672 / % possible obs: 99.1 % / Redundancy: 3.41 % / CC1/2: 0.997 / Rmerge(I) obs: 0.054 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.15→1.22 Å / Redundancy: 3.39 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 2.13 / Num. unique obs: 24551 / CC1/2: 0.726 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6L2E Resolution: 1.15→99 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refinement step | Cycle: LAST / Resolution: 1.15→99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.15→1.19 Å / Rfactor Rwork: 0.243 |