+Open data
-Basic information
Entry | Database: PDB / ID: 6iah | ||||||
---|---|---|---|---|---|---|---|
Title | Phosphatase Tt82 from Thermococcus thioreducens | ||||||
Components | Hydrolase | ||||||
Keywords | HYDROLASE / HAD superfamily / hypothetical phosphatase / docking / phosphatase assay | ||||||
Function / homology | HAD-like superfamily / hydrolase activity / Hydrolase Function and homology information | ||||||
Biological species | Thermococcus thioreducens (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å | ||||||
Authors | Brynda, J. / Smatanova, I.K. / Pachl, P. / Prudnikova, T. / Masters, R.J. / Havlickova, P. / Kascakova, B. / Brinsa, V. / Kuty, M. / Pusey, M.L. ...Brynda, J. / Smatanova, I.K. / Pachl, P. / Prudnikova, T. / Masters, R.J. / Havlickova, P. / Kascakova, B. / Brinsa, V. / Kuty, M. / Pusey, M.L. / Ng, J.D. / Rezacova, P.M. | ||||||
Funding support | Czech Republic, 1items
| ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: A novel structurally characterized haloacid dehalogenase superfamily phosphatase from Thermococcus thioreducens with diverse substrate specificity. Authors: Havlickova, P. / Brinsa, V. / Brynda, J. / Pachl, P. / Prudnikova, T. / Mesters, J.R. / Kascakova, B. / Kuty, M. / Pusey, M.L. / Ng, J.D. / Rezacova, P. / Kuta Smatanova, I. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2019 Title: A novel structurally characterized haloacid dehalogenase superfamily phosphatase from Thermococcus thioreducens with diverse substrate specificity Authors: Brynda, J. / Smatanova, I.K. / Pachl, P. / Prudnikova, T. / Masters, R.J. / Havlickova, P. / Kascakova, B. / Brinsa, V. / Kuty, M. / Pusey, M.L. / Ng, J.D. / Rezacova, P.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6iah.cif.gz | 68.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6iah.ent.gz | 52.3 KB | Display | PDB format |
PDBx/mmJSON format | 6iah.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/6iah ftp://data.pdbj.org/pub/pdb/validation_reports/ia/6iah | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 27814.553 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus thioreducens (archaea) / Gene: A3L14_07460, AMR53_08235, SAMN05216170_0457 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0Q2QQ54 | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.88 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.2 M Magnesium chloride hexahydrate, 25% w/v Polyethyleneglycol 3350, 0.1 M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→43.87 Å / Num. obs: 27374 / % possible obs: 99.9 % / Redundancy: 7.185 % / Biso Wilson estimate: 29.416 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.061 / Χ2: 1.023 / Net I/σ(I): 18.39 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Generic Helix Resolution: 1.75→43.87 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.682 / SU ML: 0.133 / SU R Cruickshank DPI: 0.1228 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.12 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.67 Å2 / Biso mean: 31.558 Å2 / Biso min: 16.59 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.75→43.87 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.75→1.796 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|