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- PDB-4mmn: Structural and biochemical analysis of type II free methionine-R-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4mmn | ||||||
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Title | Structural and biochemical analysis of type II free methionine-R-sulfoxide reductase from Thermoplasma acidophilum | ||||||
![]() | Putative uncharacterized protein Ta0848 | ||||||
![]() | OXIDOREDUCTASE / reductase | ||||||
Function / homology | GAF domain / GAF domain / GAF domain / GAF-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta / GAF domain-containing protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, H.S. / Kwak, G.H. / Lee, K.T. / Jo, C.H. / Hwang, K.Y. / Kim, H.Y. | ||||||
![]() | ![]() Title: Structural and biochemical analysis of a type II free methionine-R-sulfoxide reductase from Thermoplasma acidophilum Authors: Kim, H.S. / Kwak, G.H. / Lee, K. / Jo, C.H. / Hwang, K.Y. / Kim, H.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 225.4 KB | Display | ![]() |
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PDB format | ![]() | 183.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.8 KB | Display | ![]() |
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Full document | ![]() | 485.2 KB | Display | |
Data in XML | ![]() | 40.7 KB | Display | |
Data in CIF | ![]() | 55.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4mn7C ![]() 3mmhS 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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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17014.346 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165 Gene: Ta0848 / Plasmid: pET21b / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 64.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.17M ammonium acetate, 0.085M sodium acetate trihydrate (pH 4.6), 25.5% polyethylene glycol 4000, 15% glycerol. , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 4, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 54183 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 14.205 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 1.4 / Num. unique all: 265551 / Rsym value: 0.389 / % possible all: 73.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3MMH Resolution: 2.6→28.089 Å / SU ML: 0.42 / σ(F): 2.12 / Phase error: 26.14 / Stereochemistry target values: ML
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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: 2.6→28.089 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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