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Yorodumi- PDB-6vdg: Crystal Structure of the Y182A HisF Mutant from Thermotoga maritima -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vdg | |||||||||||||||
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Title | Crystal Structure of the Y182A HisF Mutant from Thermotoga maritima | |||||||||||||||
Components | Imidazole glycerol phosphate synthase subunit HisF | |||||||||||||||
Keywords | LYASE / Cyclase / Histidine Pathway / TIM-Barrel | |||||||||||||||
Function / homology | Function and homology information imidazole glycerol-phosphate synthase / imidazoleglycerol-phosphate synthase activity / histidine biosynthetic process / lyase activity / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Thermotoga maritima (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å | |||||||||||||||
Authors | Almeida, V.M. / Matsuyama, B.Y. / Farah, C.S. / Marana, S.R. | |||||||||||||||
Funding support | Brazil, 4items
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Citation | Journal: J.Struct.Biol. / Year: 2021 Title: Role of a high centrality residue in protein dynamics and thermal stability. Authors: Medeiros Almeida, V. / Chaudhuri, A. / Cangussu Cardoso, M.V. / Matsuyama, B.Y. / Monteiro Ferreira, G. / Goulart Trossini, G.H. / Salinas, R.K. / Loria, J.P. / Marana, S.R. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vdg.cif.gz | 113.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vdg.ent.gz | 83.1 KB | Display | PDB format |
PDBx/mmJSON format | 6vdg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/6vdg ftp://data.pdbj.org/pub/pdb/validation_reports/vd/6vdg | HTTPS FTP |
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-Related structure data
Related structure data | 1gpwS S: Starting model for refinement |
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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: 27647.750 Da / Num. of mol.: 1 / Mutation: Y182A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: hisF, TM_1036 / Production host: Escherichia coli (E. coli) References: UniProt: Q9X0C6, imidazole glycerol-phosphate synthase |
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#2: Chemical | ChemComp-PO4 / |
#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: 3.7 Å3/Da / Density % sol: 66.73 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 23% PEG 3350, 20mM Potassium Phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45851 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 3, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.45851 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→47.81 Å / Num. obs: 10873 / % possible obs: 98.6 % / Redundancy: 13.3 % / Biso Wilson estimate: 69.97 Å2 / CC1/2: 0.99 / Net I/σ(I): 17.72 |
Reflection shell | Resolution: 2.79→2.8 Å / Mean I/σ(I) obs: 1.69 / Num. unique obs: 1635 / CC1/2: 0.835 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1gpw Resolution: 2.79→45.69 Å / SU ML: 0.3883 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.1671
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.79→45.69 Å
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Refine LS restraints |
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LS refinement shell |
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