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- PDB-6t5m: Crystal structure of 2-methylisocitrate lyase (PrpB) from Pseudom... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6t5m | |||||||||
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Title | Crystal structure of 2-methylisocitrate lyase (PrpB) from Pseudomonas aeruginosa in complex with Mg(II)-pyruvate. | |||||||||
![]() | 2-methylisocitrate lyase | |||||||||
![]() | LYASE / 2-methlyisocitrate lyase / PrpB / Propionate metabolism | |||||||||
Function / homology | ![]() methylisocitrate lyase / propionate catabolic process, 2-methylcitrate cycle / methylisocitrate lyase activity / magnesium ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wijaya, A.J. / Brear, P. / Dolan, S.K. / Welch, M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of 2-methylisocitrate lyase (PrpB) from Pseudomonas aeruginosa in complex with Mg(II)-pyruvate. Authors: Wijaya, A.J. / Brear, P. / Dolan, S.K. / Welch, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 226.2 KB | Display | ![]() |
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PDB format | ![]() | 180.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.5 MB | Display | ![]() |
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Full document | ![]() | 3.5 MB | Display | |
Data in XML | ![]() | 43.5 KB | Display | |
Data in CIF | ![]() | 62.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6t4vS S: Starting model for refinement |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 32173.752 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: prpB, PA0796 / Production host: ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-PYR / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.52 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop Details: PrpB 13-15 mg/ml with 5 mM DTT 0.1 M TRIS 8.5 pH (Buffer) 20-30 %w/v PEG4K (Precipitant) 0.1-0.25 M LiSO4 (Salt) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 22, 2019 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.76→63.74 Å / Num. obs: 97480 / % possible obs: 85.7 % / Redundancy: 2.4 % / Biso Wilson estimate: 27.84 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.069 / Rrim(I) all: 0.118 / Net I/σ(I): 8.5 / Num. measured all: 234810 / Scaling rejects: 58 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6T4V Resolution: 1.76→42.493 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.09
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.06 Å2 / Biso mean: 32.4167 Å2 / Biso min: 13.07 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.76→42.493 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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