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Yorodumi- PDB-3eki: Structural insights of the Mycoplasma hyorhinis protein Mh-p37: A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eki | ||||||
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Title | Structural insights of the Mycoplasma hyorhinis protein Mh-p37: A putative thiamine pyrophosphate transporter | ||||||
Components | High affinity transport system protein p37 | ||||||
Keywords | TPP BINDING PROTEIN / Mycoplasma / p37 / TPP / cell membrane / Lipoprotein / membrane / transport / transport protein / Palmitate / extracytoplasmic thiamine binding lipoprotein / Cypl | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Sippel, K.H. / Robbins, A.H. / Reutzel, R. / McKenna, R. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2009 Title: Structural insights into the extracytoplasmic thiamine-binding lipoprotein p37 of Mycoplasma hyorhinis Authors: Sippel, K.H. / Robbins, A.H. / Reutzel, R. / Boehlein, S.K. / Namiki, K. / Goodison, S. / Agbandje-McKenna, M. / Rosser, C.J. / McKenna, R. #1: 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. / Reutzal, R. / Domsic, J. / Boehlein, S.K. / Govindasamy, L. / Agbandje-McKenna, M. / Rosser, C.J. / McKenna, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eki.cif.gz | 97.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eki.ent.gz | 72.1 KB | Display | PDB format |
PDBx/mmJSON format | 3eki.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3eki_validation.pdf.gz | 692.8 KB | Display | wwPDB validaton report |
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Full document | 3eki_full_validation.pdf.gz | 695.6 KB | Display | |
Data in XML | 3eki_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 3eki_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/3eki ftp://data.pdbj.org/pub/pdb/validation_reports/ek/3eki | HTTPS FTP |
-Related structure data
Related structure data | 3e78S 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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Details | monomeric |
-Components
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 5 types, 333 molecules
#2: Chemical | ChemComp-TPP / | ||||
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#3: Chemical | ChemComp-GOL / | ||||
#4: Chemical | #5: Chemical | ChemComp-BR / #6: 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: 2.08 Å3/Da / Density % sol: 40.91 % |
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Crystal grow | Temperature: 298 K / Method: batch / pH: 4 Details: 0.1 M Ammonium Bromide, 0.1 M Citric Acid, 40% PEG 4000, under paraffin oil, pH 4.0, Batch, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9169 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 10, 2002 |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9169 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40 Å / Num. all: 49563 / Num. obs: 47500 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rsym value: 0.071 / Net I/σ(I): 0.115 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 4759 / Rsym value: 0.288 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3E78 Resolution: 1.6→40 Å Isotropic thermal model: isotropic except for one calcium ion Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
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Displacement parameters | Biso mean: 20 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→40 Å
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Refine LS restraints |
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