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Yorodumi- PDB-3qae: 3-hydroxy-3-methylglutaryl-coenzyme A reductase of Streptococcus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qae | ||||||
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Title | 3-hydroxy-3-methylglutaryl-coenzyme A reductase of Streptococcus pneumoniae | ||||||
Components | 3-hydroxy-3-methylglutaryl-coenzyme a reductase | ||||||
Keywords | OXIDOREDUCTASE / 4-ELECTRON OXIDO-REDUCTASE | ||||||
Function / homology | Function and homology information hydroxymethylglutaryl-CoA reductase (NADH) activity / hydroxymethylglutaryl-CoA reductase / hydroxymethylglutaryl-CoA reductase (NADPH) activity / coenzyme A metabolic process / ergosterol biosynthetic process / isoprenoid biosynthetic process / peroxisomal membrane / nucleotide binding Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Zhang, L. / Feng, L. / Zhou, L. / Gui, J. / Wan, J. | ||||||
Citation | Journal: To be Published Title: 3-hydroxy-3-methylglutaryl-coenzyme A reductase of Streptococcus pneumoniae Authors: Zhang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qae.cif.gz | 92.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qae.ent.gz | 67.2 KB | Display | PDB format |
PDBx/mmJSON format | 3qae.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qae_validation.pdf.gz | 456 KB | Display | wwPDB validaton report |
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Full document | 3qae_full_validation.pdf.gz | 457.2 KB | Display | |
Data in XML | 3qae_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 3qae_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/3qae ftp://data.pdbj.org/pub/pdb/validation_reports/qa/3qae | HTTPS FTP |
-Related structure data
Related structure data | 1qaxS 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: 49845.637 Da / Num. of mol.: 1 / Mutation: A103T, G327S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: R6 / Gene: mvaA, spr1570 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8DNS5, hydroxymethylglutaryl-CoA reductase | ||
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#2: Chemical | ChemComp-CIT / | ||
#3: Chemical | ChemComp-GOL / | ||
#4: Chemical | ChemComp-NA / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 54.01 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2.0M Ammonium Sulfate, 6% PEG 400, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å | |||||||||||||||||||||
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: May 14, 2010 | |||||||||||||||||||||
Radiation | Monochromator: multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.3→24.72 Å / Num. all: 24163 / Num. obs: 24163 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.134 / Net I/σ(I): 8.8 | |||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QAX Resolution: 2.3→24.72 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.896 / SU B: 5.776 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.748 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→24.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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