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- PDB-7t7k: Structure of SPAC806.04c protein from fission yeast bound to Co2+ -

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Basic information

Entry
Database: PDB / ID: 7t7k
TitleStructure of SPAC806.04c protein from fission yeast bound to Co2+
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 / intracellular phosphate ion homeostasis / inorganic diphosphate phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / cellular detoxification / phosphatase activity / 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: 1.9 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 1.1Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)101,26119
Polymers100,0732
Non-polymers1,18717
Water13,727762
1
B: Damage-control phosphatase SPAC806.04c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4797
Polymers50,0371
Non-polymers4426
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Damage-control phosphatase SPAC806.04c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,78212
Polymers50,0371
Non-polymers74511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.654, 116.314, 151.862
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-930-

HOH

21A-946-

HOH

31A-1007-

HOH

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Components

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Protein , 1 types, 2 molecules BA

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


Mass: 50036.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: SPAC806.04c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9UT55, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases

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Non-polymers , 5 types, 779 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 762 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.3 mM SPAC806.04c, 5 mM CoCl2, 19 mM Tris-HCl (pH 7.5), and 142 mM NaCl buffer mixed with precipitant solution containing 1.8 M sodium phosphate monobasic monohydrate/potassium phosphate dibasic (pH 8.2)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→49.51 Å / Num. obs: 82654 / % possible obs: 99.9 % / Redundancy: 9.4 % / Biso Wilson estimate: 22.7 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.043 / Net I/σ(I): 12
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4480 / CC1/2: 0.75 / Rpim(I) all: 0.383 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: a low resolution structure (2.75A) obtained with a Phyre2 model for a diffferent crystal of the same protein

Resolution: 1.9→46.42 Å / SU ML: 0.183 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.3919
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1957 2074 2.51 %
Rwork0.1644 80504 -
obs0.1653 82578 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.84 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7007 0 49 762 7818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00727224
X-RAY DIFFRACTIONf_angle_d0.92189812
X-RAY DIFFRACTIONf_chiral_restr0.05491062
X-RAY DIFFRACTIONf_plane_restr0.00751250
X-RAY DIFFRACTIONf_dihedral_angle_d6.1777944
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.31481270.24985327X-RAY DIFFRACTION99.87
1.94-1.990.26461390.21365236X-RAY DIFFRACTION99.94
1.99-2.050.25211300.19475345X-RAY DIFFRACTION99.98
2.05-2.110.22411370.1815324X-RAY DIFFRACTION99.91
2.11-2.170.2281500.17125312X-RAY DIFFRACTION99.8
2.17-2.250.23131350.1635292X-RAY DIFFRACTION99.82
2.25-2.340.21851370.16285316X-RAY DIFFRACTION99.91
2.34-2.450.23971140.16895372X-RAY DIFFRACTION99.95
2.45-2.580.23551460.17225306X-RAY DIFFRACTION99.87
2.58-2.740.19771340.1815355X-RAY DIFFRACTION99.96
2.74-2.950.22311340.18945395X-RAY DIFFRACTION99.89
2.95-3.250.2011440.1715378X-RAY DIFFRACTION99.71
3.25-3.720.16961500.14315388X-RAY DIFFRACTION99.93
3.72-4.680.14211580.12085458X-RAY DIFFRACTION99.91
4.68-46.420.16831390.16775700X-RAY DIFFRACTION99.68
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)
11.226927239220.551144427711-2.634778213014.68063834528-0.3610020591625.828284995880.0229756610890.1665940585940.100117522126-0.09505856958490.03410453509490.0571420890895-0.16827085211-0.0345288845142-0.05616602586590.16049760337-0.029115373635-0.03762417713250.1153365719020.006665888398490.12955409946730.532528134130.661838589721.7542751726
21.066021551421.25128873956-0.967612899086.90648012849-6.205257719136.427029373690.0318822905984-0.05852227256070.06035156527310.3426205930620.04895906929050.203580458877-0.231281764546-0.231257865611-0.113266320080.1651937060590.04184550895630.03236884111170.188230918612-0.04051589647360.18376440705618.001598437521.208019008345.157490928
38.37411746878-3.930173460430.891058698016.74833615020.9472356048054.17158586246-0.16406989842-0.2117255861490.4338624973030.3259626186260.121413055797-0.555079872205-0.1269557786910.2189065152572.16292977582E-50.176380975408-0.0429071751574-0.02083056857530.168025456366-0.02474289729830.16863201994236.042538482730.555190078534.4286624994
41.227146406482.29178923537-3.245219056454.35307738894-6.191480961388.837757920070.0074803884914-0.06747502583350.01251864228870.043342506824-0.131473603125-0.0187363983947-0.07261337805270.2154696368650.1406166080660.1271139531690.029760048952-0.0069466660080.119697943895-0.02414068012630.14614269446527.54939503320.60754526538.4728062072
54.73192062544-0.2073362245710.394700962265.595689713092.236635211186.03232107145-0.1772606167330.364965750895-0.561683808356-0.2693924345170.1338836570140.329738674070.334336463586-0.1667248144810.1094194177750.250993128075-0.08735513299440.05109806078940.195149257410.02472807733640.24782530208114.9083204098-1.977414667622.5672557078
61.85623437597-1.39252537117-0.6771477713046.077896729584.566340988924.01240075571-0.06833855142460.0357844459435-0.1864601274820.1906695589610.00629905200320.153906910230.3741580670650.007216922769480.08258490794340.185374994104-0.01402558146170.0113994111270.1364877614790.01589067596960.1567652569222.6436419739-3.1554365527.88514032249
72.28704261411-2.26975612949-3.055979717753.14986997142.964271839284.17556678554-0.07252668893290.183740089599-0.169300656034-0.0108477329061-0.09473447191450.269243247990.049957600381-0.3023203303060.2119620659530.190078252563-0.0194464597732-0.04220628004660.1940455269810.01367916446780.23421328198917.94384086229.9658453319213.8305418147
80.6395869287170.0150572892017-0.1425884610341.28592732850.133965608651.12509679104-0.0370065183187-0.0151350889902-0.07517432390930.0530025601580.0216778980344-0.04116465410080.132035593080.08016350583690.01593542188540.1607322265040.0220003346698-0.0006639048158620.151391966284-0.006322769680410.15501016415429.85740408038.8134969486119.7457156671
92.77174367938-1.82992147477-1.214283967522.503620937041.062335352711.44495310647-0.0108998669182-0.0712647127442-0.06810861551920.07708576692910.00515618959040.1973926639590.0487093766609-0.06290296995120.01296397110060.11687327339-0.0410990224905-0.02811472239750.159002229352-0.009714602757360.142227900387-18.06244748346.933447958816.5683121766
106.01543787463.81326568757-1.041227754156.05382917892-2.545507776663.43091556581-0.01562944326620.312075876580.193663651575-0.330236967758-0.01465274091340.2386826396570.0558019271233-0.1567342669810.02479092015770.156867881380.0204214517785-0.04493875148580.192166703872-0.02399664002480.128683382213-13.249432020346.70098719893.06461867617
111.90499286988-0.4131744744360.7640282907010.655719310153-0.2271460485271.14128392072-0.0347814045598-0.2690942956810.1410137138210.155188310386-0.00548207098107-0.0910946692624-0.0455263315684-0.01823911384610.05138215016090.202265662631-0.04021371015620.006337732455460.199979061118-0.02564304967850.182556855115-1.5918443005151.428584485928.4418355558
125.5431131625-2.845439513330.7578968737252.292233800960.4098243155763.30305119386-0.0799066762069-0.975685777362-0.3733684678830.358714166490.2261820657610.1199858732780.181045481466-0.151697217592-0.1659335866580.302514272895-0.02489215403690.002354015716610.2649462494730.07180091204270.247613945149-0.36068827554939.189356334133.5695800502
131.803230685440.1847475866490.7676725035530.7086660893860.1871085365941.364805636680.0115353094876-0.2006973400490.2537612104940.0561772658533-0.0501702036532-0.0115322724148-0.0852051129930.01025359839290.02852973844650.13753486734-0.01451174053450.01300936229920.140839766918-0.02370643434510.1737245740435.7231141901355.554329657923.5223404352
142.23709947482-0.325642936843-0.02410681277923.86645610434-0.9615353725721.899680209010.0196972550956-0.058634190644-0.287956418363-0.08342595806080.003322004140750.06916698324130.1612658760260.030679137821-0.01333300182010.1533728395920.0192775592787-0.02217258548460.178765282927-0.007235364207580.1642432379736.6360527476835.547020851518.0723401366
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 165 )BA137 - 165137 - 165
66chain 'B' and (resid 166 through 193 )BA166 - 193166 - 193
77chain 'B' and (resid 194 through 235 )BA194 - 235194 - 235
88chain 'B' and (resid 236 through 438 )BA236 - 438236 - 438
99chain 'A' and (resid 0 through 74 )AB0 - 741 - 75
1010chain 'A' and (resid 75 through 108 )AB75 - 10876 - 109
1111chain 'A' and (resid 109 through 193 )AB109 - 193110 - 188
1212chain 'A' and (resid 194 through 226 )AB194 - 226189 - 221
1313chain 'A' and (resid 227 through 370 )AB227 - 370222 - 365
1414chain 'A' and (resid 371 through 438 )AB371 - 438366 - 433

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