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Yorodumi- PDB-8xxb: Crystal Structure of a triple-mutant (A69F/M124P/R127G) of halohy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8xxb | ||||||
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Title | Crystal Structure of a triple-mutant (A69F/M124P/R127G) of halohydrin dehalogenase HheD8 complexed with chloride | ||||||
Components | Short-chain dehydrogenase/reductase SDR | ||||||
Keywords | HYDROLASE / halohydrin dehalogenase | ||||||
Function / homology | Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / Short-chain dehydrogenase/reductase SDR Function and homology information | ||||||
Biological species | Thauera aminoaromatica S2 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Wan, N.W. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of a triple-mutant (A69F/M124P/R127G) of halohydrin dehalogenase HheD8 complexed with chloride Authors: Wan, N.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8xxb.cif.gz | 60.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8xxb.ent.gz | 39.4 KB | Display | PDB format |
PDBx/mmJSON format | 8xxb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xx/8xxb ftp://data.pdbj.org/pub/pdb/validation_reports/xx/8xxb | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24723.389 Da / Num. of mol.: 1 / Mutation: A69F,R127G,M124P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thauera aminoaromatica S2 (bacteria) / Gene: C665_05478 / Production host: Escherichia coli (E. coli) / References: UniProt: N6YXW4 |
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#2: Chemical | ChemComp-CL / |
#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: 3.75 Å3/Da / Density % sol: 67.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.8 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 10, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 30538 / % possible obs: 99.75 % / Redundancy: 37.5 % / Biso Wilson estimate: 38.94 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.09077 / Rpim(I) all: 0.01505 / Net I/σ(I): 38.88 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 39 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 9.21 / Num. unique obs: 1476 / CC1/2: 0.992 / Rpim(I) all: 0.09946 / % possible all: 99.39 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→44.64 Å / SU ML: 0.0683 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.8411 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.41 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→44.64 Å
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Refine LS restraints |
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LS refinement shell |
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