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Yorodumi- PDB-6t4v: Crystal structure of 2-methylisocitrate lyase (PrpB) from Pseudom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t4v | |||||||||
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Title | Crystal structure of 2-methylisocitrate lyase (PrpB) from Pseudomonas aeruginosa in apo form. | |||||||||
Components | 2-methylisocitrate lyase | |||||||||
Keywords | LYASE / 2-methlyisocitrate lyase / PrpB / Propionate metabolism | |||||||||
Function / homology | Function and homology information methylisocitrate lyase / propionate catabolic process, 2-methylcitrate cycle / methylisocitrate lyase activity / magnesium ion binding Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.807 Å | |||||||||
Authors | Wijaya, A.J. / Brear, P. / Dolan, S.K. / Welch, M. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: To Be Published Title: Crystal structure of 2-methylisocitrate lyase (PrpB) from Pseudomonas aeruginosa in apo form. Authors: Wijaya, A.J. / Brear, P. / Dolan, S.K. / Welch, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6t4v.cif.gz | 225 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t4v.ent.gz | 181.5 KB | Display | PDB format |
PDBx/mmJSON format | 6t4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6t4v_validation.pdf.gz | 464.5 KB | Display | wwPDB validaton report |
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Full document | 6t4v_full_validation.pdf.gz | 469.9 KB | Display | |
Data in XML | 6t4v_validation.xml.gz | 42.4 KB | Display | |
Data in CIF | 6t4v_validation.cif.gz | 60.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t4/6t4v ftp://data.pdbj.org/pub/pdb/validation_reports/t4/6t4v | HTTPS FTP |
-Related structure data
Related structure data | 1mumS S: Starting model for refinement |
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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 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.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: prpB, PA0796 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I5E2, methylisocitrate lyase #2: Chemical | ChemComp-PYR / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.25 Å3/Da / Density % sol: 45.4 % |
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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 PEG 4K (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: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97629 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 23, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97629 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.807→64.082 Å / Num. obs: 104256 / % possible obs: 95.2 % / Redundancy: 1.9 % / Biso Wilson estimate: 22.29 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.057 / Rrim(I) all: 0.089 / Net I/σ(I): 6.1 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 1.9 %
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MUM Resolution: 1.807→64.082 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.62
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.83 Å2 / Biso mean: 30.243 Å2 / Biso min: 9.85 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.807→64.082 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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