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- PDB-6wf7: Methylmalonyl-CoA epimerase in complex with methylmalonyl-CoA and NH4+ -
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Open data
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Basic information
Entry | Database: PDB / ID: 6wf7 | ||||||
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Title | Methylmalonyl-CoA epimerase in complex with methylmalonyl-CoA and NH4+ | ||||||
![]() | Methylmalonyl-CoA epimerase | ||||||
![]() | ISOMERASE / Epimerase / acid-base / enol / enolate | ||||||
Function / homology | ![]() methylmalonyl-CoA epimerase activity / L-methylmalonyl-CoA metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stunkard, L.M. / Benjamin, A.B. / Bower, J.B. / Huth, T.J. / Lohman, J.R. | ||||||
![]() | ![]() Title: Substrate Enolate Intermediate and Mimic Captured in the Active Site of Streptomyces coelicolor Methylmalonyl-CoA Epimerase. Authors: Stunkard, L.M. / Benjamin, A.B. / Bower, J.B. / Huth, T.J. / Lohman, J.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.7 KB | Display | ![]() |
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PDB format | ![]() | 36.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 925.6 KB | Display | ![]() |
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Full document | ![]() | 928.6 KB | Display | |
Data in XML | ![]() | 11.5 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wf6C ![]() 6wfhC ![]() 6wfiC ![]() 1jc5S 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 16059.767 Da / Num. of mol.: 1 / Mutation: M1S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 207 molecules ![](data/chem/img/NH4.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MC0.gif)
![](data/chem/img/MCA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MC0.gif)
![](data/chem/img/MCA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NH4 / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-MC0 / ( | #5: Chemical | ChemComp-MCA / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.69 Å3/Da / Density % sol: 66.66 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 50 mM sodium chloride, 100 mM Bis-Tris:HCl pH 7.0, 2.3 M ammonium sulfate, 5% PEG 400 |
-Data collection
Diffraction | Mean temperature: 80 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jul 16, 2017 / Details: MD2 Micro Diffractometer |
Diffraction measurement | Details: 1.00 degrees, 3.06 sec, detector distance 200.00 mm Method: \w scans |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Av R equivalents: 0.087 / Number: 521570 |
Reflection | Resolution: 1.55→30 Å / Num. obs: 36333 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.4 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.024 / Rrim(I) all: 0.09 / Rsym value: 0.087 / Χ2: 1.015 / Net I/av σ(I): 27 / Net I/σ(I): 11.4 / Num. measured all: 521570 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 3564 / Rsym value: 0.614 / % possible all: 100 |
Cell measurement | Reflection used: 521570 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1JC5 Resolution: 1.55→29.4 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / WRfactor Rfree: 0.1951 / WRfactor Rwork: 0.1803 / FOM work R set: 0.9022 / SU B: 0.84 / SU ML: 0.031 / SU R Cruickshank DPI: 0.0539 / SU Rfree: 0.0552 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 799 Å2 / Biso mean: 24.875 Å2 / Biso min: 12.92 Å2
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Refinement step | Cycle: final / Resolution: 1.55→29.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.591 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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