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Open data
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Basic information
Entry | Database: PDB / ID: 6x7l | ||||||
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Title | LnmK in complex with 2-nitronate-propionyl-CoA | ||||||
![]() | Bifunctional methylmalonyl-CoA:ACP acyltransferase/decarboxylase | ||||||
![]() | transferase/transferase inhibitor / ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stunkard, L.M. / Kick, B.J. / Lohman, J.R. | ||||||
![]() | ![]() Title: Structures of LnmK, a Bifunctional Acyltransferase/Decarboxylase, with Substrate Analogues Reveal the Basis for Selectivity and Stereospecificity. Authors: Stunkard, L.M. / Kick, B.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 | ![]() | 88 KB | Display | ![]() |
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PDB format | ![]() | 63.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6x7mC ![]() 6x7nC ![]() 6x7oC ![]() 6x7pC ![]() 4hzoS 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
#1: Protein | Mass: 35380.387 Da / Num. of mol.: 1 / Mutation: M1S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-ALA / ![]() | ||||
#3: Chemical | ChemComp-KFV / [ | ||||
#4: Chemical | ChemComp-SO4 / ![]() #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.11 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 150 mM lithium sulfate, 100 mM Bis-Tris pH 7.0, 28% PEG 3350 Temp details: room temperature |
-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: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 17, 2016 / Details: MD2 microdifractometer |
Diffraction measurement | Details: 1.00 degrees, -1.0 sec, detector distance 180.26 mm Method: \w scans |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Av R equivalents: 0.079 / Number: 709330 |
Reflection | Resolution: 1.77→30 Å / Num. obs: 34783 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 20.4 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.018 / Rrim(I) all: 0.081 / Rsym value: 0.079 / Χ2: 1.035 / Net I/av σ(I): 38.674 / Net I/σ(I): 11.1 / Num. measured all: 709330 |
Reflection shell | Resolution: 1.77→1.83 Å / Redundancy: 20.5 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 14.583 / Num. unique obs: 3310 / Rsym value: 0.257 / % possible all: 98.3 |
Cell measurement | Reflection used: 709330 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4HZO Resolution: 1.77→29.94 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.141 / SU ML: 0.069 / SU R Cruickshank DPI: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.106 / 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: 95.75 Å2 / Biso mean: 23.525 Å2 / Biso min: 10.76 Å2
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Refinement step | Cycle: final / Resolution: 1.77→29.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.771→1.817 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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