[English] 日本語
Yorodumi- PDB-8awp: Crystal structure of a manganese-containing cupin (tm1459) from T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8awp | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a manganese-containing cupin (tm1459) from Thermotoga maritima, variant 208 (V19I/R23H/M38I/I60F/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: 1.595 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 | 8awp.cif.gz | 66.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8awp.ent.gz | 43.4 KB | Display | PDB format |
PDBx/mmJSON format | 8awp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8awp_validation.pdf.gz | 430.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8awp_full_validation.pdf.gz | 430.4 KB | Display | |
Data in XML | 8awp_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 8awp_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/8awp ftp://data.pdbj.org/pub/pdb/validation_reports/aw/8awp | HTTPS FTP |
-Related structure data
Related structure data | 8awnC 8awoC 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: 13165.018 Da / Num. of mol.: 2 / Mutation: V19I, R23H, M38I, I60F, 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: 1.89 Å3/Da / Density % sol: 34.83 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 14.2 mg/ml protein concentration 1.6M Sodium citrate tribasic dihydrate pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.595→45.77 Å / Num. obs: 27169 / % possible obs: 99.41 % / Redundancy: 6.6 % / Biso Wilson estimate: 22.26 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06499 / Rpim(I) all: 0.02775 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.595→1.652 Å / Rmerge(I) obs: 0.7128 / Mean I/σ(I) obs: 2.33 / Num. unique obs: 2590 / CC1/2: 0.837 / CC star: 0.955 / Rpim(I) all: 0.2985 / % possible all: 96.23 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1vj2 Resolution: 1.595→45.77 Å / SU ML: 0.1448 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.8737 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: 26.58 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.595→45.77 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|