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- PDB-7u1y: Structure of SPAC806.04c protein from fission yeast bound to AlF4... -

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Basic information

Entry
Database: PDB / ID: 7u1y
TitleStructure of SPAC806.04c protein from fission yeast bound to AlF4 and Co2+
ComponentsDamage-control phosphatase SPAC806.04c
KeywordsHYDROLASE / metal-dependent phosphatase / Domain of Unknown Function 89 (DUF89)
Function / homology
Function and homology information


fructose 6-phosphate aldolase activity / fructose-1-phosphatase activity / inorganic diphosphate phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / intracellular phosphate ion homeostasis / cellular detoxification / phosphatase activity / DNA damage response / metal ion binding / nucleus / cytosol
Similarity search - Function
Transcription Elongation Factor S-II; Chain A - #60 / 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 / Transcription Elongation Factor S-II; Chain A / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
sucrose / TETRAFLUOROALUMINATE ION / : / : / Damage-control phosphatase SPAC806.04c
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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
DepositionFeb 22, 2022Deposition 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,6396
Polymers50,0371
Non-polymers6025
Water7,656425
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.721, 133.721, 56.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein / Sugars , 2 types, 2 molecules A

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


Mass: 50036.734 Da / Num. of mol.: 1
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
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 429 molecules

#3: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2.53 Å3/Da / Density % sol: 51.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M NaCL, 0.1 M HEPES-NaOH (pH 7.0), 20% (w/v) PEG 6,000; cryprotectant: 0.2M NaCL, 0.1 M HEPES-NaOH (pH 7.0), 22% (w/v) PEG 6,000, 25% (w/v) sucrose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.605 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.605 Å / Relative weight: 1
ReflectionResolution: 1.81→47.28 Å / Num. obs: 43687 / % possible obs: 95.9 % / Redundancy: 11.4 % / Biso Wilson estimate: 19.9 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.021 / Net I/σ(I): 26.6
Reflection shellResolution: 1.81→1.85 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 4.1 / Num. unique obs: 1572 / CC1/2: 0.925 / Rpim(I) all: 0.144 / % possible all: 59

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7U1V

7u1v


Resolution: 1.81→47.28 Å / SU ML: 0.1737 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 18.2918
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1818 2145 4.91 %
Rwork0.1561 41539 -
obs0.1574 43684 95.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.54 Å2
Refinement stepCycle: LAST / Resolution: 1.81→47.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3530 0 31 425 3986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713667
X-RAY DIFFRACTIONf_angle_d0.97774986
X-RAY DIFFRACTIONf_chiral_restr0.056546
X-RAY DIFFRACTIONf_plane_restr0.0087633
X-RAY DIFFRACTIONf_dihedral_angle_d6.237495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.860.2873860.22641769X-RAY DIFFRACTION61.02
1.86-1.90.22351450.19432440X-RAY DIFFRACTION85.6
1.9-1.950.17641320.17662631X-RAY DIFFRACTION92.13
1.95-2.010.20771460.1622831X-RAY DIFFRACTION98.35
2.01-2.080.19321500.16562849X-RAY DIFFRACTION99.97
2.08-2.150.22441470.15762886X-RAY DIFFRACTION99.93
2.15-2.240.20571370.162902X-RAY DIFFRACTION99.93
2.24-2.340.2121530.16832861X-RAY DIFFRACTION99.97
2.34-2.460.20161650.16612881X-RAY DIFFRACTION100
2.46-2.610.19061320.16112872X-RAY DIFFRACTION100
2.62-2.820.20121320.16692928X-RAY DIFFRACTION100
2.82-3.10.19651740.17062875X-RAY DIFFRACTION99.93
3.1-3.550.17971340.14622922X-RAY DIFFRACTION99.93
3.55-4.470.14731610.13472904X-RAY DIFFRACTION100
4.47-47.280.14331510.14392988X-RAY DIFFRACTION99.97
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)
12.841822501560.113268547927-1.485719615333.056925710632.219981181624.43063813528-0.132952244927-0.29277987491-0.1282803639490.266599028796-0.1871750201950.1740727184820.4354466917490.06008989685320.3116584277830.173869948546-0.0126777673048-0.06544468866130.202508229744-0.006244512941880.24205015461339.443027826427.313568925529.5984553592
24.825885774392.00457312531.038536603146.533456006680.8828124890483.43088873692-0.0774131773431-0.395328006540.3272889524080.3089830822060.0186008179741-0.201356458087-0.10425873662-0.002489397839370.03531181396960.1196067998960.0372871691946-0.003390876101160.164342578558-0.03814389643880.11582614415546.17490832247.703506475548.1479745942
35.08929999630.253576414392-2.680659194612.66640930084-1.538946038236.19107306312-0.06354731344870.331061843240.534248090264-0.137823442544-0.007157195525990.160149031175-0.198816782133-0.4326420699960.0578331886540.1793287939820.0474571171292-0.1146233914750.190621756544-0.04116362028170.2785183363838.462952153940.434386118427.1130429412
41.087657547130.242032456430.5263690286443.459629507872.179344365212.36933638418-0.01378456083460.0982335862887-0.0027885168872-0.0700391560850.04508724688920.0114069328299-0.01572764954460.0805350766099-0.03760297001880.1054051233460.0141168846817-0.007517421771410.141054218613-0.007007499073940.16434846015447.844588688343.736382201837.1868833432
55.50769321811-3.23276499046-1.732211506595.114691828622.187918192013.63791249552-0.0134950737758-0.0478556458731-0.145711543749-0.004610497754790.0111712886013-0.1490140692990.1343006068390.252208627834-0.006758456040290.111221966904-0.0242361767216-0.03256918791870.106202309160.002132617160780.1012717296874.43549742925.843469682143.8556502677
66.55510128319-1.84865011091-4.654810542583.937722495081.805447878587.04290072291-0.3045626088930.0803707052957-0.472704670560.1459676602370.120469731796-0.3219435826670.4660424558090.2210885315220.1972562909260.207510647385-0.0247222195965-0.01170900178420.177741982393-0.0343529391190.20017716098771.626554697215.476076734835.423551167
70.3928748986460.4999267453720.8189046515415.235196661132.434961268038.046650932210.10080338049-0.263062952607-0.1831188802590.7915393017880.03295578028670.09464072172510.3780648756790.18616688418-0.09455737796490.229912712245-0.08127186542040.008296438703560.2673159047180.01159824952580.321368244658.899266295719.025995107444.8117125537
82.33644034853-0.421288346911-0.1856392442831.502152739870.1554017834150.50226710664-0.04869709754670.109649198124-0.00844405282046-0.1063139200610.00528733191068-0.100199058033-0.03407610944320.01237968941810.05350180728330.15121901068-0.00858964185449-0.01381767325930.167781852507-0.01362682340650.11807290382167.852624933227.990644427431.2933558409
92.564291726350.2993303146861.644165859160.5130485884550.3758880272981.57255906909-0.0603211590713-0.05158465662180.111187023196-0.06309431703940.024318541713-0.00108697069003-0.0396765143372-0.05761364689930.06307162763120.157988862484-0.01138582407490.01131603588220.132283339592-0.004247769670230.15008332690469.741400553236.659930641136.9022647939
101.310598408250.4505515084950.5545489165641.844596744560.005930237199021.04774178968-0.03482964208680.08843094515180.0132264675644-0.1658286198490.006090270910650.1167456740410.0381784153704-0.1051758149850.02617203900460.1911664959930.000570483338078-0.02438345147050.21413833996-0.03950341079430.13808833891754.970676858723.517878543524.1055628962
115.369572850312.17596990395-1.979028426595.17929517952-1.366394601214.593793568820.0611960198758-0.130100133114-0.1683421852970.4787525203120.002798372900060.4342434308630.593817806562-0.995517795188-0.06319391518930.270907303323-0.09770289527380.0074313389350.354642178147-0.04124042171280.20490533107152.146525894812.458662690734.2471142466
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: UNK / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 26 )0 - 261 - 27
22chain 'A' and (resid 27 through 74 )27 - 7428 - 75
33chain 'A' and (resid 75 through 108 )75 - 10876 - 109
44chain 'A' and (resid 109 through 136 )109 - 136110 - 137
55chain 'A' and (resid 137 through 171 )137 - 171138 - 172
66chain 'A' and (resid 172 through 193 )172 - 193173 - 194
77chain 'A' and (resid 194 through 227 )194 - 227195 - 228
88chain 'A' and (resid 228 through 288 )228 - 288229 - 289
99chain 'A' and (resid 289 through 337 )289 - 337290 - 338
1010chain 'A' and (resid 338 through 411 )338 - 411339 - 412
1111chain 'A' and (resid 412 through 438 )412 - 438413 - 439

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