+Open data
-Basic information
Entry | Database: PDB / ID: 5hwp | ||||||
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Title | MvaS with acetylated Cys115 in complex with coenzyme A | ||||||
Components | Hydroxymethylglutaryl-CoA synthase | ||||||
Keywords | TRANSFERASE / MvaS / Myxococcus xanthus / Biosynthesis | ||||||
Function / homology | Function and homology information hydroxymethylglutaryl-CoA synthase / hydroxymethylglutaryl-CoA synthase activity / farnesyl diphosphate biosynthetic process, mevalonate pathway / acetyl-CoA metabolic process / ergosterol biosynthetic process Similarity search - Function | ||||||
Biological species | Myxococcus xanthus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Bock, T. / Kasten, J. / Blankenfeldt, W. | ||||||
Citation | Journal: Chembiochem / Year: 2016 Title: Crystal Structure of the HMG-CoA Synthase MvaS from the Gram-Negative Bacterium Myxococcus xanthus. Authors: Bock, T. / Kasten, J. / Muller, R. / Blankenfeldt, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hwp.cif.gz | 156.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hwp.ent.gz | 131.4 KB | Display | PDB format |
PDBx/mmJSON format | 5hwp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hwp_validation.pdf.gz | 719.7 KB | Display | wwPDB validaton report |
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Full document | 5hwp_full_validation.pdf.gz | 721.8 KB | Display | |
Data in XML | 5hwp_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 5hwp_validation.cif.gz | 29.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/5hwp ftp://data.pdbj.org/pub/pdb/validation_reports/hw/5hwp | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 44555.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myxococcus xanthus (strain DK 1622) (bacteria) Strain: DK 1622 / Gene: mvaS, MXAN_4267 / Plasmid: pET19m / Production host: Escherichia coli (E. coli) References: UniProt: Q1D4I1, hydroxymethylglutaryl-CoA synthase |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-COA / |
#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: 2.42 Å3/Da / Density % sol: 49.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.2 M (NH4)2SO4, 0.2 disodium tartrate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å | ||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 13, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→28.87 Å / Num. obs: 23581 / % possible obs: 100 % / Redundancy: 40.5 % / Biso Wilson estimate: 12.32 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.482 / Rpim(I) all: 0.075 / Rrim(I) all: 0.488 / Net I/σ(I): 12.4 / Num. measured all: 956150 / Scaling rejects: 17 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→28.867 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 16.89 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.75 Å2 / Biso mean: 13.6919 Å2 / Biso min: 4.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→28.867 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %
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