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Yorodumi- PDB-3e78: Structure determination of the cancer-associated Mycoplasma hyorh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3.0E+78 | ||||||
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Title | Structure determination of the cancer-associated Mycoplasma hyorhinis protein Mh-p37 | ||||||
Components | High affinity transport system protein p37 | ||||||
Keywords | TPP Binding Protein / Mycoplasma / p37 / TPP / Cell membrane / Lipoprotein / Membrane / Palmitate / Transport | ||||||
Function / homology | Function and homology information regulation of cell migration / regulation of protein phosphorylation / host cell cytoplasm / plasma membrane Similarity search - Function | ||||||
Biological species | Mycoplasma hyorhinis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SIRAS / Resolution: 1.9 Å | ||||||
Authors | Sippel, K.H. / Robbins, A.H. / Reutzel, R. / Domsic, J. / McKenna, R. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Structure determination of the cancer-associated Mycoplasma hyorhinis protein Mh-p37. Authors: Sippel, K.H. / Robbins, A.H. / Reutzel, R. / Domsic, J. / Boehlein, S.K. / Govindasamy, L. / Agbandje-McKenna, M. / Rosser, C.J. / McKenna, R. #1: Journal: To be Published Title: A magic triangle for experimental phasing of macromolecules Authors: Beck, T. / Krasauskas, A. / Gruene, T. / Sheldrick, G.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e78.cif.gz | 90.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e78.ent.gz | 68 KB | Display | PDB format |
PDBx/mmJSON format | 3e78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/3e78 ftp://data.pdbj.org/pub/pdb/validation_reports/e7/3e78 | HTTPS FTP |
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-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: 46117.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasma hyorhinis (bacteria) / Gene: p37 / Plasmid: pET31p37 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P15363 |
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#2: Chemical | ChemComp-TPP / |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-CL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.69 % |
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Crystal grow | Temperature: 298 K / Method: batch / pH: 3 Details: 0.1 M Ammonium Bromide, O.1 M Citric Acid, 40% PEG 4000, 9% N-decyl-beta-D-maltoside detergent , pH 3.0, Batch, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 5, 2008 / Details: Osmic mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. obs: 29894 / % possible obs: 96.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 26.427 Å2 / Rsym value: 0.067 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.9→1.98 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 5 / Num. unique all: 2860 / Rsym value: 0.376 / % possible all: 93.2 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.9→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure
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Displacement parameters | Biso mean: 32.694 Å2 | |||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→25 Å
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Refine LS restraints |
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