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Yorodumi- PDB-8hjy: Crystal structure of a cupin protein (tm1459, H52A/H58E/F104W mut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hjy | |||||||||
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Title | Crystal structure of a cupin protein (tm1459, H52A/H58E/F104W mutant) in copper (Cu) substituted form | |||||||||
Components | Cupin_2 domain-containing protein | |||||||||
Keywords | 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 Function and homology information | |||||||||
Biological species | Thermotoga maritima MSB8 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å | |||||||||
Authors | Matsumoto, R. / Kurisu, G. / Fujieda, N. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Chem Sci / Year: 2023 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: Journal: Chem Sci / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hjy.cif.gz | 158.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hjy.ent.gz | 125.7 KB | Display | PDB format |
PDBx/mmJSON format | 8hjy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hjy_validation.pdf.gz | 432.3 KB | Display | wwPDB validaton report |
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Full document | 8hjy_full_validation.pdf.gz | 433.1 KB | Display | |
Data in XML | 8hjy_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 8hjy_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hj/8hjy ftp://data.pdbj.org/pub/pdb/validation_reports/hj/8hjy | HTTPS FTP |
-Related structure data
Related structure data | 8hjxC 8hjzC 6l2eS S: Starting model for refinement 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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Unit cell |
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-Components
#1: Protein | Mass: 13390.303 Da / Num. of mol.: 2 / Mutation: H52A/H58E/F104W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Gene: TM_1459 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9X1H0 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.07 Å3/Da / Density % sol: 40.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% w/v Jeffamine ED-2001, 0.1M MES pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
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: 1.18→99 Å / Num. obs: 141051 / % possible obs: 99 % / Redundancy: 3.45 % / CC1/2: 0.995 / Rmerge(I) obs: 0.073 / Net I/σ(I): 8.78 |
Reflection shell | Resolution: 1.18→1.25 Å / Redundancy: 3.42 % / Rmerge(I) obs: 0.789 / Mean I/σ(I) obs: 2.02 / Num. unique obs: 22674 / CC1/2: 0.706 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6L2E Resolution: 1.18→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: 1.18→99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.18→1.22 Å / Rfactor Rwork: 0.272 |