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- PDB-8awn: Crystal structure of a manganese-containing cupin (tm1459) from T... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8awn | ||||||
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Title | Crystal structure of a manganese-containing cupin (tm1459) from Thermotoga maritima, variant C106Q | ||||||
![]() | Cupin_2 domain-containing protein | ||||||
![]() | METAL BINDING PROTEIN / cupin / alkene cleavage / amino acid oxidation | ||||||
Function / homology | Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / metal ion binding / Cupin type-2 domain-containing protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Grininger, C. / Steiner, K. / Gruber, K. / Pavkov-Keller, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Engineering TM1459 for Stabilisation against Inactivation by Amino Acid Oxidation Authors: Grill, B. / Pavkov-Keller, T. / Grininger, C. / Darnhofer, B. / Gruber, K. / Hall, M. / Schwab, H. / Steiner, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.4 KB | Display | ![]() |
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PDB format | ![]() | 48 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 403.8 KB | Display | ![]() |
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Full document | ![]() | 403.9 KB | Display | |
Data in XML | ![]() | 8.3 KB | Display | |
Data in CIF | ![]() | 11.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8awoC ![]() 8awpC ![]() 1vj2S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13154.059 Da / Num. of mol.: 1 / Mutation: C106Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8 Gene: TM_1459 Production host: ![]() ![]() References: UniProt: Q9X1H0 |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.44 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 1 M LiCl 0.1 M citrate pH 4.0 20 % PEG6000 16 mg/ml protein concentration |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→37.66 Å / Num. obs: 56128 / % possible obs: 99.89 % / Redundancy: 8.9 % / Biso Wilson estimate: 18.71 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.04822 / Rpim(I) all: 0.01703 / Net I/σ(I): 24.33 |
Reflection shell | Resolution: 1.45→1.502 Å / Rmerge(I) obs: 0.9108 / Mean I/σ(I) obs: 1.84 / Num. unique obs: 2932 / CC1/2: 0.731 / CC star: 0.919 / Rpim(I) all: 0.3633 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1vj2 Resolution: 1.45→37.66 Å / SU ML: 0.1308 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.7792 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.99 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→37.66 Å
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Refine LS restraints |
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LS refinement shell |
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