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- PDB-6iah: Phosphatase Tt82 from Thermococcus thioreducens -

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Basic information

Entry
Database: PDB / ID: 6iah
TitlePhosphatase Tt82 from Thermococcus thioreducens
ComponentsHydrolase
KeywordsHYDROLASE / HAD superfamily / hypothetical phosphatase / docking / phosphatase assay
Function / homologyHAD-like superfamily / hydrolase activity / Hydrolase
Function and homology information
Biological speciesThermococcus thioreducens (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsBrynda, 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
OrganizationGrant numberCountry
Grant Agency of the Czech Republic17-24321S Czech Republic
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
DepositionNov 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,13611
Polymers27,8151
Non-polymers32110
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.330, 117.000, 33.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Hydrolase / / Phosphoglycolate phosphatase / HAD superfamily


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 ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.75-1.87.1340.4733.6319970.9640.5199.7
1.8-1.846.6510.3784.2719050.9760.4199.6
1.84-1.97.2670.3095.4918960.9850.33399.9
1.9-1.967.5540.2536.8718500.990.27299.9
1.96-2.027.4920.1968.517670.9930.211100
2.02-2.097.4690.16110.3317200.9950.173100
2.09-2.177.4310.13312.2616650.9950.14399.9
2.17-2.267.2390.11813.4116180.9960.127100
2.26-2.366.6420.09715.2115400.9970.10599.9
2.36-2.477.3830.08318.1114840.9980.089100
2.47-2.617.5730.07320.4214120.9980.07899.9
2.61-2.777.5670.06224.2713510.9990.06799.9
2.77-2.967.3790.05527.7512500.9990.0699.9
2.96-3.27.1140.04731.7611840.9990.05100
3.2-3.56.2650.03835.6911020.9990.041100
3.5-3.917.3550.03243.779980.9990.035100
3.91-4.527.2730.03147.988880.9990.03499.9
4.52-5.536.9050.03146.337770.9990.034100
5.53-7.836.1590.033435990.9990.03799.7
7.83-43.876.3050.0349.563710.9980.03398.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
ArcimboldoLITEphasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 1340 4.9 %RANDOM
Rwork0.1854 ---
obs0.1874 26033 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 81.67 Å2 / Biso mean: 31.558 Å2 / Biso min: 16.59 Å2
Baniso -1Baniso -2Baniso -3
1--3.32 Å2-0 Å2-0 Å2
2---2.88 Å20 Å2
3---6.2 Å2
Refinement stepCycle: final / Resolution: 1.75→43.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1967 0 10 231 2208
Biso mean--40.92 41.64 -
Num. residues----240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192137
X-RAY DIFFRACTIONr_bond_other_d0.0020.022019
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.962893
X-RAY DIFFRACTIONr_angle_other_deg0.97234647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9475264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.02623.017116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53715378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7821523
X-RAY DIFFRACTIONr_chiral_restr0.1080.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022475
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02534
LS refinement shellResolution: 1.75→1.796 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 97 -
Rwork0.34 1898 -
all-1995 -
obs--99.6 %

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