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Yorodumi- PDB-7eru: Crystal structure of L-histidine decarboxylase (C57S mutant) from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7eru | ||||||
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Title | Crystal structure of L-histidine decarboxylase (C57S mutant) from Photobacterium phosphoreum | ||||||
Components | Histidine decarboxylase | ||||||
Keywords | LYASE / decarboxylase | ||||||
Function / homology | Function and homology information histidine decarboxylase / histidine decarboxylase activity / carboxylic acid metabolic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Photobacterium phosphoreum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Oda, Y. / Nakata, K. / Yamaguchi, H. / Kashiwagi, T. / Miyano, H. / Mizukoshi, T. | ||||||
Citation | Journal: J.Biochem. / Year: 2022 Title: Structural insights into the enhanced thermostability of cysteine substitution mutants of L-histidine decarboxylase from Photobacterium phosphoreum. Authors: Oda, Y. / Nakata, K. / Miyano, H. / Mizukoshi, T. / Yamaguchi, H. / Kashiwagi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7eru.cif.gz | 89.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7eru.ent.gz | 65.6 KB | Display | PDB format |
PDBx/mmJSON format | 7eru.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7eru_validation.pdf.gz | 431.2 KB | Display | wwPDB validaton report |
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Full document | 7eru_full_validation.pdf.gz | 437.7 KB | Display | |
Data in XML | 7eru_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 7eru_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/7eru ftp://data.pdbj.org/pub/pdb/validation_reports/er/7eru | HTTPS FTP |
-Related structure data
Related structure data | 7ervC 3f9tS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 42190.547 Da / Num. of mol.: 1 / Mutation: C57S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photobacterium phosphoreum (bacteria) / Gene: hdc / Production host: Escherichia coli (E. coli) / References: UniProt: Q1JU62, histidine decarboxylase |
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Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: PEG1000, sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→100 Å / Num. obs: 11390 / % possible obs: 99.9 % / Redundancy: 18.7 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 27.7 |
Reflection shell | Resolution: 2.85→2.93 Å / Num. unique obs: 11390 / CC1/2: 0.949 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F9T Resolution: 2.85→45.13 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.893 / SU B: 14.1 / SU ML: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 202.56 Å2 / Biso mean: 57.263 Å2 / Biso min: 23.99 Å2
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Refinement step | Cycle: final / Resolution: 2.85→45.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.85→2.924 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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