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Yorodumi- PDB-4mv2: Crystal structure of plu4264 protein from Photorhabdus luminescens -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mv2 | |||||||||
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Title | Crystal structure of plu4264 protein from Photorhabdus luminescens | |||||||||
Components | plu4264 | |||||||||
Keywords | UNKNOWN FUNCTION / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro / cupin | |||||||||
Function / homology | Function and homology information Polyketide biosynthesis protein CurC, predicted / Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta Similarity search - Domain/homology | |||||||||
Biological species | Photorhabdus luminescens subsp. laumondii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.349 Å | |||||||||
Authors | Michalska, K. / Li, H. / Jedrzejczak, R. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Weerth, S. / Thomas, M.G. / Phillips Jr., G.N. / Joachimiak, A. ...Michalska, K. / Li, H. / Jedrzejczak, R. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Weerth, S. / Thomas, M.G. / Phillips Jr., G.N. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Enzyme Discovery for Natural Product Biosynthesis (NatPro) | |||||||||
Citation | Journal: Proteins / Year: 2015 Title: Structure of a cupin protein Plu4264 from Photorhabdus luminescens subsp. laumondii TTO1 at 1.35 angstrom resolution. Authors: Weerth, R.S. / Michalska, K. / Bingman, C.A. / Yennamalli, R.M. / Li, H. / Jedrzejczak, R. / Wang, F. / Babnigg, G. / Joachimiak, A. / Thomas, M.G. / Phillips, G.N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mv2.cif.gz | 135.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mv2.ent.gz | 114.2 KB | Display | PDB format |
PDBx/mmJSON format | 4mv2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mv2_validation.pdf.gz | 439.8 KB | Display | wwPDB validaton report |
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Full document | 4mv2_full_validation.pdf.gz | 441.9 KB | Display | |
Data in XML | 4mv2_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 4mv2_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mv/4mv2 ftp://data.pdbj.org/pub/pdb/validation_reports/mv/4mv2 | 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
#1: Protein | Mass: 15567.780 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photorhabdus luminescens subsp. laumondii (bacteria) Strain: TT01 / Gene: plu4264 / Plasmid: pMCSG81 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: Q7MZL9 #2: Chemical | #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | |
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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: 2.77 Å3/Da / Density % sol: 55.61 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M Li2SO4, 0.1 M Tris/HCl 8.5, 25% PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2012 / Details: mirrors |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→30 Å / Num. all: 76260 / Num. obs: 76134 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 26.8 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.891 / Mean I/σ(I) obs: 2 / Num. unique all: 3769 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.349→24.898 Å / SU ML: 0.12 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 15.92 / Stereochemistry target values: ML / Details: hydrogen atoms have been added at riding positions
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.349→24.898 Å
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Refine LS restraints |
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LS refinement shell |
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