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- PDB-7t7o: Structure of SPAC806.04c protein from fission yeast covalently bo... -

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Basic information

Entry
Database: PDB / ID: 7t7o
TitleStructure of SPAC806.04c protein from fission yeast covalently bound to BeF3
ComponentsDamage-control phosphatase SPAC806.04c
KeywordsHYDROLASE / metal-dependent phosphatase / Domain of Unknown Function 89 (DUF89)
Function / homology
Function and homology information


fructose-1-phosphatase activity / fructose 6-phosphate aldolase activity / inorganic diphosphate phosphatase activity / intracellular phosphate ion homeostasis / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / cellular detoxification / phosphatase activity / DNA damage response / nucleus / metal ion binding / cytosol
Similarity search - Function
Damage-control phosphatase ARMT1 / Damage-control phosphatase ARMT1-like, metal-binding domain / Damage-control phosphatase ARMT1-like, metal-binding domain superfamily / Damage-control phosphatase ARMT1-like domain
Similarity search - Domain/homology
: / PHOSPHATE ION / Damage-control phosphatase SPAC806.04c
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsJacewicz, A. / Sanchez, A.M. / Shuman, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM126945 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Fission yeast Duf89 and Duf8901 are cobalt/nickel-dependent phosphatase-pyrophosphatases that act via a covalent aspartyl-phosphate intermediate.
Authors: Sanchez, A.M. / Jacewicz, A. / Shuman, S.
History
DepositionDec 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Damage-control phosphatase SPAC806.04c
A: Damage-control phosphatase SPAC806.04c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,4165
Polymers100,2032
Non-polymers2133
Water4,197233
1
B: Damage-control phosphatase SPAC806.04c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1612
Polymers50,1021
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Damage-control phosphatase SPAC806.04c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2563
Polymers50,1021
Non-polymers1542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.937, 116.495, 151.573
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-716-

HOH

21A-716-

HOH

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Components

#1: Protein Damage-control phosphatase SPAC806.04c / Sugar phosphate phosphatase SPAC806.04c


Mass: 50101.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9UT55, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.6 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.3 mM SPAC806.04c protein in 5 mM CoCl2, 5 mM BeCl2, 15 mM NaF, 15 mM Tris-HCl (pH 7.5), and 112 mM NaCl-containing buffer mixed with equla volume of 1.8 M sodium phosphate monobasic ...Details: 0.3 mM SPAC806.04c protein in 5 mM CoCl2, 5 mM BeCl2, 15 mM NaF, 15 mM Tris-HCl (pH 7.5), and 112 mM NaCl-containing buffer mixed with equla volume of 1.8 M sodium phosphate monobasic monohydrate/potassium phosphate dibasic (pH 8.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.60601 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.60601 Å / Relative weight: 1
ReflectionResolution: 2.16→49.08 Å / Num. obs: 55903 / % possible obs: 99.9 % / Redundancy: 11.4 % / Biso Wilson estimate: 22.6 Å2 / CC1/2: 0.989 / Rpim(I) all: 0.11 / Net I/σ(I): 7.6
Reflection shellResolution: 2.16→2.22 Å / Redundancy: 11 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4532 / CC1/2: 0.629 / Rpim(I) all: 0.487 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7T7K

7t7k


Resolution: 2.16→46.35 Å / SU ML: 0.2765 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.6102
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2349 2641 2.49 %
Rwork0.2018 103322 -
obs0.2026 55843 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.02 Å2
Refinement stepCycle: LAST / Resolution: 2.16→46.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7019 0 7 233 7259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00767211
X-RAY DIFFRACTIONf_angle_d0.93879791
X-RAY DIFFRACTIONf_chiral_restr0.05031064
X-RAY DIFFRACTIONf_plane_restr0.00741250
X-RAY DIFFRACTIONf_dihedral_angle_d8.2383952
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.20.28941830.26865406X-RAY DIFFRACTION99.71
2.2-2.240.30111220.25535479X-RAY DIFFRACTION99.68
2.24-2.290.28571510.25915387X-RAY DIFFRACTION99.37
2.29-2.340.33021150.25635372X-RAY DIFFRACTION98.99
2.34-2.390.30461490.25485447X-RAY DIFFRACTION99.27
2.39-2.450.25141540.24445441X-RAY DIFFRACTION99.98
2.45-2.520.2621440.23075451X-RAY DIFFRACTION99.73
2.52-2.590.23821260.23335433X-RAY DIFFRACTION99.87
2.59-2.680.21131540.22955388X-RAY DIFFRACTION99.73
2.68-2.770.30481700.22895493X-RAY DIFFRACTION99.81
2.77-2.880.28711340.23775386X-RAY DIFFRACTION99.59
2.88-3.010.30311410.23675434X-RAY DIFFRACTION99.59
3.01-3.170.29931470.22215436X-RAY DIFFRACTION99.32
3.17-3.370.17141190.19915450X-RAY DIFFRACTION99.71
3.37-3.630.21211370.17775478X-RAY DIFFRACTION99.96
3.63-40.20031020.16225471X-RAY DIFFRACTION99.89
4-4.570.17831460.1475413X-RAY DIFFRACTION99.96
4.57-5.760.17681240.15365499X-RAY DIFFRACTION99.86
5.76-46.350.211230.18485458X-RAY DIFFRACTION99.79
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6758057520330.656105383788-1.879407476455.94991415325-0.2507269351395.539979737530.06655302577310.09394072027480.0683798312306-0.05763492729460.07031121018170.0929129317286-0.349565268629-0.0140481988512-0.08035676511710.165735582548-0.0284214346727-0.03697108156430.179299311159-0.005145837042050.14349087611430.076125652930.8200973721.8455272406
21.187879531781.0287159023-0.951473141587.98742484989-7.774726411168.55276711529-0.0249573989433-0.1450790905050.02641394786140.506150985522-0.05658720217090.045641440749-0.335080801872-0.1794418044910.08199579346730.208783603550.01703872907970.03944885418640.224612126125-0.05722863240310.21072284023717.811001092321.2760452145.4130574431
37.89704613774-2.243118672720.641781355556.678145931740.7742832043316.42443269034-0.061702765218-0.1934047185870.4813215342180.04676546888930.149959174947-0.730657881232-0.1713571240920.576751639423-0.07088251035940.183801551218-0.03561232659580.01387320238090.193268649791-0.05210810671730.2180178388135.634819902930.600322807534.4820117112
41.498002244551.10733938266-2.677421012023.09909956791-4.511816799797.650403941760.000313328460769-0.0213247875942-0.08011577711570.0425166193898-0.09465042455750.01758393443580.06535538138020.02635718125590.1044663965260.1434986737170.001093686439430.0176828012550.176256184664-0.02603821343190.17130276056527.382024524920.608356726438.5898466595
55.00391292410.8197550571391.70147298927.421430139521.292591124051.85559817463-0.0202976696498-0.00919347240182-0.03121923684710.0393735213574-0.101962286580.6144130034110.320336576703-0.3888126700540.1503944477040.271290166311-0.05421208145340.08035739579470.2833430597490.07205159800480.18408785102413.45049975931.0786707139925.6232496088
61.696733929910.341163330299-0.4810832329542.642493790742.659842313544.26799440374-0.2498755722860.127430925398-0.384462090350.1922827343370.02421325367550.2861895618180.6408045723090.01116963296730.1849964632920.3147076367860.005885071712340.05066054464640.225754150075-0.008037474308370.2611268655122.166023488-5.013912288648.6295720853
74.403868962260.186081058769-2.46431437275.089548219171.798283895076.66231522603-0.06144935460820.250736740477-0.298265695559-0.143644841244-0.08152985030860.5807820285760.209251252737-0.6543069696770.1526775785720.2535152290990.017421550401-0.06962769723140.2592581092940.02862039295390.29231016699814.125882558511.955208672315.7502425695
81.478250614930.5823676266041.265979591151.54142529418-1.003937743592.78835534121-0.07529505711880.0819521241783-0.2445727736780.008425850040890.0854013493501-0.2682951003330.8045996560870.5046935418120.001557435247310.3037639564970.05489253609020.0234408290750.190695596195-0.01054252563360.2759599362432.95147066011.3260546385813.8278323871
90.5916042640650.076960354063-0.2167301188131.345556799390.03259566138241.01512857578-0.0513503481590.0140690662611-0.0515452758009-0.0495551686922-0.0136619097316-0.054278763950.1251873300550.04799336810860.06310496693970.2415681809030.007453618823160.006613079200330.234334403417-0.003334368239880.21526216204429.46645742649.5543249657319.882347709
101.13257513022-0.2964384120170.06133760261910.6288229791210.06948084033130.568643138361-0.00995877338459-0.0126997546662-0.00107754087558-0.0233530577089-0.008464336881710.02928293781950.0309481022116-0.03119216166390.01819537959820.247529662054-0.05511699998880.02988744562240.2299278110840.001780168377820.229365087633-10.253374001349.092760416419.2039504405
113.68350913831-4.46666384331-0.7093441942165.690366035460.2645300156967.97601134375-0.217487348245-0.936897874029-0.6820841799380.8817925865580.4516885488580.708473465180.141861877669-0.31245173174-0.2297091104730.496573626125-0.07278810372940.05916793755040.2730298841580.04835580340440.431807299834-0.80289005848639.331497498433.5705364486
120.9001936875-0.1831405076460.01871420692390.935106209438-0.02805152576871.16046836087-0.00488556290371-0.06568109367930.03771241991190.008047345436130.05593722137-0.0529018911341-0.04008987268430.1750210712-0.04854168686190.182855109935-0.008853630646240.01363791184950.251777972864-0.005693254579480.1986564069845.8242030351949.280067076121.7309175114
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 1 through 26 )BA1 - 261 - 26
22chain 'B' and (resid 27 through 74 )BA27 - 7427 - 74
33chain 'B' and (resid 75 through 108 )BA75 - 10875 - 108
44chain 'B' and (resid 109 through 136 )BA109 - 136109 - 136
55chain 'B' and (resid 137 through 159 )BA137 - 159137 - 159
66chain 'B' and (resid 160 through 193 )BA160 - 193160 - 193
77chain 'B' and (resid 194 through 227 )BA194 - 227194 - 227
88chain 'B' and (resid 228 through 251 )BA228 - 251228 - 251
99chain 'B' and (resid 252 through 438 )BA252 - 438252 - 438
1010chain 'A' and (resid 0 through 193 )AB0 - 1931 - 188
1111chain 'A' and (resid 194 through 226 )AB194 - 226189 - 221
1212chain 'A' and (resid 227 through 438 )AB227 - 438222 - 433

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