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- PDB-8tkz: Structure of fission yeast Duf89 protein bound to Co2+ and PO4 -

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Basic information

Entry
Database: PDB / ID: 8tkz
TitleStructure of fission yeast Duf89 protein bound to Co2+ and PO4
ComponentsDamage-control phosphatase SPCC1393.13
KeywordsHYDROLASE / METAL-DEPENDENT PHOSPHATASE / DOMAIN OF UNKNOWN FUNCTION 89 (DUF89)
Function / homology
Function and homology information


protein carboxyl O-methyltransferase activity / : / fructose-1-phosphatase activity / fructose 6-phosphate aldolase 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
: / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / Damage-control phosphatase SPCC1393.13
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsJacewicz, A. / Sanchez, A.M. / Shuman, S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM126945 United States
Department of Energy (DOE, United States)DE-SC0012704 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To Be Published
Title: Structure of fission yeast Duf89 protein bound to Co2+ and PO4
Authors: Jacewicz, A. / Sanchez, A.M. / Shuman, S.
History
DepositionJul 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Damage-control phosphatase SPCC1393.13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,10712
Polymers50,2601
Non-polymers84711
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.109, 91.163, 106.813
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules B

#1: Protein Damage-control phosphatase SPCC1393.13


Mass: 50260.191 Da / Num. of mol.: 1 / Mutation: D252N
Source method: isolated from a genetically manipulated source
Details: Ser0 remains after tag removal. Asp252Asn is an engineered mutation. Residues 198 to 211 were not modeled due to disorder.
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: SPCC1393.13 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O94725

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Non-polymers , 8 types, 195 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.67 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: A solution containing 0.24 mM Duf89-D252N protein, 5 mM CoCl2, 10 mM sodium pyrophosphate (pH 6.5), 18.2 mM Tris-HCl (pH 7.5), 136.2 mM NaCl, and 0.455 mM EDTA was preincubated on ice for 30 ...Details: A solution containing 0.24 mM Duf89-D252N protein, 5 mM CoCl2, 10 mM sodium pyrophosphate (pH 6.5), 18.2 mM Tris-HCl (pH 7.5), 136.2 mM NaCl, and 0.455 mM EDTA was preincubated on ice for 30 min. Aliquots were then mixed with equal volume of precipitant solution containing 0.01 M ZnSO4, 0.2 M MES (pH 6.5), and 25% (v/v) PEG-550 MME. Cryoprotectant: 100% paraffin oil

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jun 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 34041 / % possible obs: 99.1 % / Redundancy: 8 % / Biso Wilson estimate: 30.12 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.039 / Net I/σ(I): 25.8
Reflection shellResolution: 2.06→2.1 Å / Rmerge(I) obs: 1.138 / Mean I/σ(I) obs: 2 / Num. unique obs: 1677 / CC1/2: 0.618 / CC star: 0.874 / Rpim(I) all: 0.425 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→28.42 Å / SU ML: 0.2291 / Cross valid method: FREE R-VALUE / σ(F): 0.1 / Phase error: 23.1795
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2271 1829 5.86 %
Rwork0.1736 29362 -
obs0.1767 31191 91.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.57 Å2
Refinement stepCycle: LAST / Resolution: 2.06→28.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3439 0 42 184 3665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01283562
X-RAY DIFFRACTIONf_angle_d1.18044820
X-RAY DIFFRACTIONf_chiral_restr0.0645518
X-RAY DIFFRACTIONf_plane_restr0.0092615
X-RAY DIFFRACTIONf_dihedral_angle_d8.4711470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.120.3231270.24122060X-RAY DIFFRACTION84.8
2.12-2.180.29231250.22892085X-RAY DIFFRACTION85.93
2.18-2.250.28581280.222081X-RAY DIFFRACTION86.53
2.25-2.330.2931350.20492124X-RAY DIFFRACTION87.19
2.33-2.420.26431360.19562173X-RAY DIFFRACTION89.08
2.42-2.530.27831380.18832168X-RAY DIFFRACTION89.35
2.53-2.670.2621430.19932236X-RAY DIFFRACTION91.78
2.67-2.830.28311360.19342250X-RAY DIFFRACTION92.19
2.83-3.050.29281470.19882332X-RAY DIFFRACTION93.94
3.05-3.360.23911480.19362370X-RAY DIFFRACTION96.4
3.36-3.840.20251490.15762403X-RAY DIFFRACTION97
3.84-4.840.1711540.1312480X-RAY DIFFRACTION98.32
4.84-28.420.17831630.15272600X-RAY DIFFRACTION98.89
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)
12.811658623940.488136195383-1.473955848982.30333993588-0.2006276474832.75592083983-0.0151654477653-0.0637121391614-0.04393257265490.09674003722090.04446903613140.02906598023410.112861103687-0.0522428390309-0.01934498390660.146282852180.0161812306762-0.03796062144760.158439834445-0.02746749895130.1629333230569.6231786574413.7053451422-1.51168201455
24.686458281681.029005394090.4369226423275.862902244552.097627801655.74243804576-0.05459578401460.337927733416-0.281462412384-0.209750225756-0.4204299914490.3982150831170.508707625271-0.474757020310.4227410834430.439030831722-0.112695832988-0.03107163019110.2763078222310.001004491677840.417930641072-2.30536796814-12.2792431473-20.1208753604
32.871937095781.22351789136-0.1379979394311.74012268896-1.839581386023.139450390160.117413694540.439622383624-0.593749672404-0.516760040248-0.05704803678520.3137771838730.358313810316-0.439951671441-0.008706045579170.486441886546-0.0111418077189-0.05753466183870.439417936769-0.1342473909040.3811040804418.28783517833-8.49292785542-31.2138679784
42.075566788390.5663149930510.0840968036542.662834532740.6455062155541.794748321460.08839045837610.109504242557-0.224737037951-0.161352004883-0.0520856051109-0.07219932186580.335415795706-0.0367840151806-0.05550431683410.2735691557160.0283719628228-0.04215487104030.216823311842-0.05827825224840.17711678336913.7942807632-3.02842150115-18.1028605092
Refinement TLS group

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

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'B' and (resid 0 through 140 )0 - 1401 - 141
22chain 'B' and (resid 141 through 173 )141 - 173142 - 174
33chain 'B' and (resid 174 through 241 )174 - 241175 - 228
44chain 'B' and (resid 242 through 442 )242 - 442229 - 429

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