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Yorodumi- PDB-6hr7: HMG-CoA reductase from Methanothermococcus thermolithotrophicus a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hr7 | ||||||
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Title | HMG-CoA reductase from Methanothermococcus thermolithotrophicus apo form at 2.4 A resolution | ||||||
Components | HMG-CoA reductase | ||||||
Keywords | OXIDOREDUCTASE / HMG-CoA / Mevalonate biosynthesis / statins / cholesterol biosynthesis / isoprenoids / structural rearrangement. | ||||||
Function / homology | Function and homology information hydroxymethylglutaryl-CoA reductase (NADPH) / hydroxymethylglutaryl-CoA reductase (NADPH) activity / coenzyme A metabolic process / isoprenoid biosynthetic process Similarity search - Function | ||||||
Biological species | Methanothermococcus thermolithotrophicus DSM 2095 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Wagner, T. / Voegeli, B. / Erb, T.J. / Shima, S. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Febs Lett. / Year: 2019 Title: Crystal structure of archaeal HMG-CoA reductase: insights into structural changes of the C-terminal helix of the class-I enzyme. Authors: Vogeli, B. / Shima, S. / Erb, T.J. / Wagner, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hr7.cif.gz | 318.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hr7.ent.gz | 261.5 KB | Display | PDB format |
PDBx/mmJSON format | 6hr7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hr7_validation.pdf.gz | 656 KB | Display | wwPDB validaton report |
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Full document | 6hr7_full_validation.pdf.gz | 660.6 KB | Display | |
Data in XML | 6hr7_validation.xml.gz | 28.5 KB | Display | |
Data in CIF | 6hr7_validation.cif.gz | 38.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/6hr7 ftp://data.pdbj.org/pub/pdb/validation_reports/hr/6hr7 | HTTPS FTP |
-Related structure data
Related structure data | 6hr8C 1dq8S 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 46637.793 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: / Source: (gene. exp.) Methanothermococcus thermolithotrophicus DSM 2095 (archaea) Tissue: / / Cell: / / Cell line: / / Gene: HMGR / Organ: / / Plasmid: pET-28b / Details (production host): / / Cell (production host): / / Organ (production host): / / Production host: Escherichia coli BL21 (bacteria) / Tissue (production host): / / Variant (production host): BL21-AI References: UniProt: A0A4V8GZY0*PLUS, hydroxymethylglutaryl-CoA reductase (NADPH) |
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-Non-polymers , 7 types, 54 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-P6G / | #7: Chemical | ChemComp-CL / | #8: Water | ChemComp-HOH / | |
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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: 2.27 Å3/Da / Density % sol: 45.91 % / Description: Long rod shape |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: HMGR was concentrated until 10 mg/ml by using an Amicon Ultra-4 Centrifugation filter (30 kDa cut-off) (Millipore) and centrifuged for 5 minute to remove any aggregates and dust. 0.7 ul of ...Details: HMGR was concentrated until 10 mg/ml by using an Amicon Ultra-4 Centrifugation filter (30 kDa cut-off) (Millipore) and centrifuged for 5 minute to remove any aggregates and dust. 0.7 ul of protein sample was spotted on a 96-well 2-drop MRC Crystallization Plates (Molecular Dimensions, Suffolk, UK) and 0.7 ul of reservoir solution was mixed. The best crystals were obtained after several month using a solution containing 40% v/v PEG 400, 100 mM Tris PH 8.5 and 200 mM Li2SO4. Temp details: Temperature fluctation of +/- 3 degree |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97662 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97662 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→42.613 Å / Num. obs: 33184 / % possible obs: 99.7 % / Redundancy: 10.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.029 / Rrim(I) all: 0.094 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 10.8 % / Rmerge(I) obs: 1.177 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4821 / CC1/2: 0.634 / Rpim(I) all: 0.375 / Rrim(I) all: 1.236 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DQ8 Resolution: 2.4→42.613 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.76
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→42.613 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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