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Yorodumi- PDB-1hw8: COMPLEX OF THE CATALYTIC PORTION OF HUMAN HMG-COA REDUCTASE WITH ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hw8 | ||||||
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Title | COMPLEX OF THE CATALYTIC PORTION OF HUMAN HMG-COA REDUCTASE WITH COMPACTIN (ALSO KNOWN AS MEVASTATIN) | ||||||
Components | HMG-COA REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / protein-inhibitor complex | ||||||
Function / homology | Function and homology information hydroxymethylglutaryl-CoA reductase (NADPH) / hydroxymethylglutaryl-CoA reductase (NADPH) activity / sterol biosynthetic process / GTPase regulator activity / coenzyme A binding / negative regulation of amyloid-beta clearance / Cholesterol biosynthesis / EGR2 and SOX10-mediated initiation of Schwann cell myelination / coenzyme A metabolic process / isoprenoid biosynthetic process ...hydroxymethylglutaryl-CoA reductase (NADPH) / hydroxymethylglutaryl-CoA reductase (NADPH) activity / sterol biosynthetic process / GTPase regulator activity / coenzyme A binding / negative regulation of amyloid-beta clearance / Cholesterol biosynthesis / EGR2 and SOX10-mediated initiation of Schwann cell myelination / coenzyme A metabolic process / isoprenoid biosynthetic process / peroxisomal membrane / cholesterol biosynthetic process / negative regulation of protein secretion / NADPH binding / regulation of ERK1 and ERK2 cascade / Activation of gene expression by SREBF (SREBP) / long-term synaptic potentiation / visual learning / negative regulation of protein catabolic process / PPARA activates gene expression / endoplasmic reticulum membrane / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / difference fourier / Resolution: 2.1 Å | ||||||
Authors | Istvan, E.S. / Deisenhofer, J. | ||||||
Citation | Journal: Science / Year: 2001 Title: Structural mechanism for statin inhibition of HMG-CoA reductase. Authors: Istvan, E.S. / Deisenhofer, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hw8.cif.gz | 305.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hw8.ent.gz | 243.9 KB | Display | PDB format |
PDBx/mmJSON format | 1hw8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hw8_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 1hw8_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 1hw8_validation.xml.gz | 57.1 KB | Display | |
Data in CIF | 1hw8_validation.cif.gz | 79.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/1hw8 ftp://data.pdbj.org/pub/pdb/validation_reports/hw/1hw8 | HTTPS FTP |
-Related structure data
Related structure data | 1hw9C 1hwiC 1hwjC 1hwkC 1hwlC 1dqaS 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: 50021.523 Da / Num. of mol.: 4 / Fragment: CATALYTIC PORTION / Mutation: M485I Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH COMPACTIN (MEVASTATIN), NATURAL PRODUCT OF PENICILLIUM CITRINUM Source: (gene. exp.) Homo sapiens (human) / Gene: HMGCR / Plasmid: PGEX-CS / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA References: UniProt: P04035, hydroxymethylglutaryl-CoA reductase (NADPH) #2: Chemical | ChemComp-114 / ( #3: Chemical | #4: 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: 2.1 Å3/Da / Density % sol: 42 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: microseeding / pH: 7.5 Details: PEG 4000, ammonium acetate, glycerol, DTT, Hepes, Microseeding, pH 7.5 at 294 K | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / Method: batch method / Details: used microseeding | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.942 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 2, 2000 / Details: mirror |
Radiation | Monochromator: horizontally bent Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.942 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→100 Å / Num. all: 89730 / Num. obs: 89730 / % possible obs: 91.6 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.08→2.12 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 1.6 / Num. unique all: 3268 / % possible all: 66.8 |
Reflection | *PLUS |
-Processing
Software |
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Refinement | Method to determine structure: difference fourier Starting model: pdb entry 1dqa Resolution: 2.1→43.13 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2470315.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(I): -3 / Stereochemistry target values: Engh & Huber / Details: ncs-restraints were used
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.2 Å2 / ksol: 0.372 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→43.13 Å
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Refine LS restraints |
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Refine LS restraints NCS | Weight Biso : 5 / Weight position: 250 | ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 2.2 % / Rfactor obs: 0.191 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 36.8 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.26 / % reflection Rfree: 2.5 % / Rfactor Rwork: 0.236 |