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- PDB-5ox7: Structure of P110 from Mycoplasma genitalium at 2.4A with potassi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ox7 | ||||||
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Title | Structure of P110 from Mycoplasma genitalium at 2.4A with potassium ion | ||||||
![]() | Mgp-operon protein 3 | ||||||
![]() | CELL ADHESION / Mycoplasma genitalium protein D | ||||||
Function / homology | MgpC adhesin / Mgp-operon protein 3, C-terminal domain / MgpC adhesin / MGP3 C-terminal domain / cell adhesion / plasma membrane / : / Mgp-operon protein 3![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Aparicio, D. / Fita, I. | ||||||
![]() | ![]() Title: Mycoplasma genitalium adhesin P110 binds sialic-acid human receptors. Authors: Aparicio, D. / Torres-Puig, S. / Ratera, M. / Querol, E. / Pinol, J. / Pich, O.Q. / Fita, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 360.3 KB | Display | ![]() |
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PDB format | ![]() | 295.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.1 KB | Display | ![]() |
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Full document | ![]() | 449.4 KB | Display | |
Data in XML | ![]() | 33.4 KB | Display | |
Data in CIF | ![]() | 46.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6r3tC ![]() 6r41C ![]() 6r43C ![]() 5mzb C: citing same article ( 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
#1: Protein | Mass: 99555.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 33530 / G-37 / NCTC 10195 / Gene: MG192 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-K / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.67 Å3/Da / Density % sol: 66.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350 21% 0.2M Tri-potassium citrate |
-Data collection
Diffraction | Mean temperature: 78 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 25, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97895 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→62.54 Å / Num. obs: 56936 / % possible obs: 99.6 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 1.8 / Num. measured obs: 28274 / Num. unique all: 8248 / CC1/2: 0.706 / Rpim(I) all: 0.469 / Rrim(I) all: 0.877 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5MZB ![]() 5mzb Resolution: 2.4→62.54 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 18.797 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.21 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.37 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→62.54 Å
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Refine LS restraints |
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