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- PDB-7ncy: Dual specificity phosphatase from Sulfolobales Beppu filamentous ... -

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Basic information

Entry
Database: PDB / ID: 7ncy
TitleDual specificity phosphatase from Sulfolobales Beppu filamentous virus 3
ComponentsDual specificity phosphatase
KeywordsVIRAL PROTEIN / phosphatase
Function / homology
Function and homology information


protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / negative regulation of MAPK cascade / cytoplasm
Similarity search - Function
Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Putative dual specificity phosphatase
Similarity search - Component
Biological speciesSulfolobales Beppu filamentous virus 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsWelin, M. / Akutsu, M. / Hakansson, M. / Al-Karadaghi, S. / Jasilionis, A. / Nordberg Karlsson, E.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)685778European Union
CitationJournal: To Be Published
Title: Dual specificity phosphatase from Sulfolobales Beppu filamentous virus 3
Authors: Welin, M. / Akutsu, M. / Hakansson, M. / Al-Karadaghi, S. / Jasilionis, A. / Nordberg Karlsson, E.
History
DepositionJan 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Derived calculations / Structure summary
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity phosphatase
B: Dual specificity phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7396
Polymers32,4372
Non-polymers3024
Water2,756153
1
A: Dual specificity phosphatase
hetero molecules

B: Dual specificity phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7396
Polymers32,4372
Non-polymers3024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-x+y+1,-z+1/31
Buried area1370 Å2
ΔGint-19 kcal/mol
Surface area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.620, 59.620, 167.123
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Dual specificity phosphatase / Phosphatase


Mass: 16218.692 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobales Beppu filamentous virus 3 / Gene: SBFV3_gp41 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: A0A3Q8Q3X3
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.69 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Bis-tris pH 5.5 23% PEG 3350 0.2M ammonium acetate 10 mM NiCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9783 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9783 Å / Relative weight: 1
ReflectionResolution: 2→51.63 Å / Num. obs: 24113 / % possible obs: 99.8 % / Redundancy: 29.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.211 / Rpim(I) all: 0.039 / Rrim(I) all: 0.215 / Χ2: 0.98 / Net I/σ(I): 12.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 30.8 % / Rmerge(I) obs: 2.204 / Num. unique obs: 1755 / CC1/2: 0.736 / Rpim(I) all: 0.402 / Rrim(I) all: 2.241 / Χ2: 1.01 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2→49.381 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.173 / SU ML: 0.11 / Cross valid method: FREE R-VALUE / ESU R: 0.15 / ESU R Free: 0.143
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2196 1101 4.577 %
Rwork0.1765 22953 -
all0.178 --
obs-24054 99.759 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.263 Å2
Baniso -1Baniso -2Baniso -3
1--0.752 Å2-0.376 Å2-0 Å2
2---0.752 Å2-0 Å2
3---2.439 Å2
Refinement stepCycle: LAST / Resolution: 2→49.381 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2163 0 14 153 2330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132269
X-RAY DIFFRACTIONr_bond_other_d00.0172096
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.6413077
X-RAY DIFFRACTIONr_angle_other_deg1.2381.5834819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4785268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.38121.032126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76715359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.5771516
X-RAY DIFFRACTIONr_chiral_restr0.0540.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022535
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02541
X-RAY DIFFRACTIONr_nbd_refined0.2160.2473
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.21981
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21060
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.2968
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2141
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0010.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2480.254
X-RAY DIFFRACTIONr_nbd_other0.2680.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1860.217
X-RAY DIFFRACTIONr_mcbond_it1.9373.4361069
X-RAY DIFFRACTIONr_mcbond_other1.9383.4361069
X-RAY DIFFRACTIONr_mcangle_it2.825.1341338
X-RAY DIFFRACTIONr_mcangle_other2.8195.1361339
X-RAY DIFFRACTIONr_scbond_it2.4053.6961200
X-RAY DIFFRACTIONr_scbond_other2.4043.6961201
X-RAY DIFFRACTIONr_scangle_it3.7425.4271739
X-RAY DIFFRACTIONr_scangle_other3.7415.4271740
X-RAY DIFFRACTIONr_lrange_it5.52740.6492602
X-RAY DIFFRACTIONr_lrange_other5.41440.3162569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.281980.2691652X-RAY DIFFRACTION99.9429
2.052-2.1080.235630.2631624X-RAY DIFFRACTION99.9408
2.108-2.1690.256690.2391585X-RAY DIFFRACTION100
2.169-2.2360.301840.231522X-RAY DIFFRACTION100
2.236-2.3090.239720.2091503X-RAY DIFFRACTION100
2.309-2.390.295660.2011473X-RAY DIFFRACTION100
2.39-2.480.256430.1941416X-RAY DIFFRACTION100
2.48-2.5810.207530.1791357X-RAY DIFFRACTION100
2.581-2.6960.236760.1691283X-RAY DIFFRACTION100
2.696-2.8270.203700.1691218X-RAY DIFFRACTION99.9224
2.827-2.9790.22580.171202X-RAY DIFFRACTION100
2.979-3.160.193500.1641121X-RAY DIFFRACTION100
3.16-3.3770.24600.1741034X-RAY DIFFRACTION100
3.377-3.6460.174500.1661011X-RAY DIFFRACTION100
3.646-3.9930.191450.147922X-RAY DIFFRACTION100
3.993-4.4610.175370.133831X-RAY DIFFRACTION100
4.461-5.1460.242300.137760X-RAY DIFFRACTION100
5.146-6.2890.211440.184637X-RAY DIFFRACTION100
6.289-8.8380.243210.184530X-RAY DIFFRACTION100
8.838-49.3810.189120.216272X-RAY DIFFRACTION84.0237

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