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Open data
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Basic information
Entry | Database: PDB / ID: 6se5 | ||||||
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Title | Y830A mutant from Mycoplasma genitalium P110 adhesin | ||||||
![]() | Mgp-operon protein 3 | ||||||
![]() | SUGAR BINDING PROTEIN / Adhesion complex | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Fita, I. / Aparicio, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Mycoplasma genitalium complex Authors: Fita, I. / Aparicio, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 361.8 KB | Display | ![]() |
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PDB format | ![]() | 292.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.6 KB | Display | ![]() |
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Full document | ![]() | 438.1 KB | Display | |
Data in XML | ![]() | 33.2 KB | Display | |
Data in CIF | ![]() | 48.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6r3tS 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: 100379.078 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 / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.69 Å3/Da / Density % sol: 66.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 23 % PEG 3350 0.2 M Tri-potassium citrate |
-Data collection
Diffraction | Mean temperature: 98 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→91.93 Å / Num. obs: 70593 / % possible obs: 98.8 % / Redundancy: 4.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.058 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.21→2.24 Å / Rmerge(I) obs: 1.55 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 3502 / CC1/2: 0.49 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6R3T Resolution: 2.21→32.3 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.919 / SU R Cruickshank DPI: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.174 / SU Rfree Blow DPI: 0.158 / SU Rfree Cruickshank DPI: 0.16
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Displacement parameters | Biso max: 213.96 Å2 / Biso mean: 85.63 Å2 / Biso min: 50.3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.43 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.21→32.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.21→2.23 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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Refinement TLS params. | Method: refined / Origin x: 8.6155 Å / Origin y: 31.9443 Å / Origin z: 48.2728 Å
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Refinement TLS group | Selection details: { A|* } |