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- PDB-5wpk: Structure of the class II 3-hydroxy-3-methylglutaryl-CoA reductas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5wpk | ||||||
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Title | Structure of the class II 3-hydroxy-3-methylglutaryl-CoA reductase from Streptococcus pneumoniae bound to HMG-CoA and in a partially closed conformation | ||||||
![]() | 3-hydroxy-3-methylglutaryl coenzyme A reductase | ||||||
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Function / homology | ![]() hydroxymethylglutaryl-CoA reductase (NADH) activity / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Miller, B.R. / Kung, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Features and Domain Movements Controlling Substrate Binding and Cofactor Specificity in Class II HMG-CoA Reductase. Authors: Miller, B.R. / Kung, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 178.5 KB | Display | ![]() |
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PDB format | ![]() | 137.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5wpjC ![]() 3qaeS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 46457.820 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: mvaA, mvaA_1, mvaA_3, AWW74_09880, ERS019416_00185, ERS019687_00346, ERS020135_00205, ERS020138_01692, ERS020141_01867, ERS020145_01986, ERS020146_01579, ERS020155_00051, ERS020158_01777, ...Gene: mvaA, mvaA_1, mvaA_3, AWW74_09880, ERS019416_00185, ERS019687_00346, ERS020135_00205, ERS020138_01692, ERS020141_01867, ERS020145_01986, ERS020146_01579, ERS020155_00051, ERS020158_01777, ERS020520_02006, ERS020525_01644, ERS020528_00536, ERS020531_01915, ERS020532_00514, ERS020539_01756, ERS020726_02213, ERS020726_02223, ERS020822_01277, ERS021354_03805, ERS021629_07183, ERS021733_05462, ERS232524_02161, ERS367337_00780, ERS409444_00519 Plasmid: pSKB3 Details (production host): N-terminal hexa-his-tag with kanomycin cassette Production host: ![]() ![]() ![]() References: UniProt: A0A0D6J7E8, UniProt: Q8DNS5*PLUS, ![]() #2: Chemical | ![]() #3: Chemical | ![]() #4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.06 % |
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100 mM Tris, pH 8.5, 100-250 mM lithium sulfate, 15-25% PEG4000 Temp details: Room Temperature |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 30, 2017 |
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.3→19.241 Å / Num. obs: 36792 / % possible obs: 98.17 % / Redundancy: 3.5 % / CC1/2: 0.987 / Rmerge(I) obs: 0.1514 / Net I/σ(I): 6.48 |
Reflection shell | Resolution: 2.3→2.382 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.5832 / Mean I/σ(I) obs: 1.84 / Num. unique obs: 3643 / CC1/2: 0.676 / % possible all: 97.98 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 3QAE Resolution: 2.3→19.241 Å / Cross valid method: FREE R-VALUE / σ(F): 478.83 / Phase error: 27.84
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→19.241 Å
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Refine LS restraints |
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LS refinement shell |
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