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- PDB-5sv6: Crystal structure of MxaJ from Methlophaga aminisulfidivorans MPT -
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Open data
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Basic information
Entry | Database: PDB / ID: 5sv6 | ||||||
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Title | Crystal structure of MxaJ from Methlophaga aminisulfidivorans MPT | ||||||
![]() | Extracellular solute-binding protein, family 3 | ||||||
![]() | UNKNOWN FUNCTION / MxaJ / Methlophaga aminisulfidivorans / MDH / PBP | ||||||
Function / homology | methanol catabolic process / Methanol oxidation system protein MoxJ / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / periplasmic space / BROMIDE ION / Extracellular solute-binding protein, family 3![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Choi, J.M. / Lee, S.H. | ||||||
![]() | ![]() Title: MxaJ structure reveals a periplasmic binding protein-like architecture with unique secondary structural elements Authors: Choi, J.M. / Cao, T.P. / Kim, S.W. / Lee, K.H. / Lee, S.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.5 KB | Display | ![]() |
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PDB format | ![]() | 50.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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: 32839.879 Da / Num. of mol.: 1 / Fragment: UNP residues 12-281 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: MP / Gene: mxaJ / Plasmid: pET28a(+) / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-BR / |
#3: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.79 Å3/Da / Density % sol: 31.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2M sodium bromide, 20%(w/v) PEG 3350, 10%(w/v) glycerol, 0.1M Tris HCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2010 |
Radiation | Monochromator: DCM Si(111) crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→50 Å / Num. obs: 18684 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.9 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 0.69 |
Reflection shell | Resolution: 1.92→1.95 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 16.049 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 1.92→29.728 Å
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Refine LS restraints |
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LS refinement shell |
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