[English] 日本語
Yorodumi- PDB-8awo: Crystal structure of a manganese-containing cupin (tm1459) from T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8awo | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a manganese-containing cupin (tm1459) from Thermotoga maritima, variant AIFQ (Y7A/M38I/Y83F/C106Q) | ||||||
Components | Cupin_2 domain-containing protein | ||||||
Keywords | 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 Function and homology information | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Grininger, C. / Steiner, K. / Gruber, K. / Pavkov-Keller, T. | ||||||
Funding support | Austria, 1items
| ||||||
Citation | Journal: Chem Ing Tech / Year: 2023 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8awo.cif.gz | 67.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8awo.ent.gz | 44.8 KB | Display | PDB format |
PDBx/mmJSON format | 8awo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8awo_validation.pdf.gz | 431.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8awo_full_validation.pdf.gz | 433.5 KB | Display | |
Data in XML | 8awo_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 8awo_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/8awo ftp://data.pdbj.org/pub/pdb/validation_reports/aw/8awo | HTTPS FTP |
-Related structure data
Related structure data | 8awnC 8awpC 1vj2S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 13027.924 Da / Num. of mol.: 2 / Mutation: Y7A, M38I, Y83F, C106Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) Strain: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8 Gene: TM_1459 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q9X1H0 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.88 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 8 mg/ml protein concentration 0.1 M Tris pH 8.5 2 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→34.6 Å / Num. obs: 23041 / % possible obs: 99.75 % / Redundancy: 6.4 % / Biso Wilson estimate: 23.91 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.08215 / Rpim(I) all: 0.03552 / Net I/σ(I): 12.75 |
Reflection shell | Resolution: 1.7→1.761 Å / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2.82 / Num. unique obs: 2219 / CC1/2: 0.836 / CC star: 0.954 / Rpim(I) all: 0.2754 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1vj2 Resolution: 1.7→34.6 Å / SU ML: 0.2019 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.1977 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→34.6 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|