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- PDB-7t7n: Structure of SPCC1393.13 protein from fission yeast -

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Basic information

Entry
Database: PDB / ID: 7t7n
TitleStructure of SPCC1393.13 protein from fission yeast
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
1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / PHOSPHATE ION / Damage-control phosphatase SPCC1393.13
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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

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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)50,5343
Polymers50,2611
Non-polymers2732
Water4,432246
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.720, 88.221, 48.257
Angle α, β, γ (deg.)90.000, 101.067, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Damage-control phosphatase SPCC1393.13 / Sugar phosphate phosphatase SPCC1393.13


Mass: 50261.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Ser 0 remains after tag removal. Three first residues from N-terminus (SMG) are disordered , therefore they were not modeled.
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: SPCC1393.13 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O94725, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
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: 2.59 Å3/Da / Density % sol: 52.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.24 mM SPCC1393.13 protein in a buffer containing 5 mM CoCl2, 10 mM sodium pyrophosphate (pH 6.5), 18 mM Tris-HCl (pH 7.5), and 135 mM NaCl mixed with precipitant solution containing 0.1 M ...Details: 0.24 mM SPCC1393.13 protein in a buffer containing 5 mM CoCl2, 10 mM sodium pyrophosphate (pH 6.5), 18 mM Tris-HCl (pH 7.5), and 135 mM NaCl mixed with precipitant solution containing 0.1 M citric acid (pH 5.0) and 20% (w/v) PEG-6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.5895 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5895 Å / Relative weight: 1
ReflectionResolution: 1.99→47.36 Å / Num. obs: 31632 / % possible obs: 90.5 % / Redundancy: 6.1 % / Biso Wilson estimate: 18.4 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.048 / Net I/σ(I): 12.7
Reflection shellResolution: 1.99→2.05 Å / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1004 / CC1/2: 0.797 / Rpim(I) all: 0.311

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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→47.36 Å / SU ML: 0.187 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.6736
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2003 3062 5 %
Rwork0.16 58127 -
obs0.1621 31625 89.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.11 Å2
Refinement stepCycle: LAST / Resolution: 2→47.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3530 0 17 246 3793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00833655
X-RAY DIFFRACTIONf_angle_d0.98754963
X-RAY DIFFRACTIONf_chiral_restr0.0584538
X-RAY DIFFRACTIONf_plane_restr0.0082636
X-RAY DIFFRACTIONf_dihedral_angle_d6.9475479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.329410.3442762X-RAY DIFFRACTION26.17
2.03-2.060.2714850.26631734X-RAY DIFFRACTION57.24
2.06-2.10.2999970.22381968X-RAY DIFFRACTION65.6
2.1-2.130.29251510.21122205X-RAY DIFFRACTION76.74
2.13-2.180.26831340.20442470X-RAY DIFFRACTION83.62
2.18-2.220.25971150.19182717X-RAY DIFFRACTION91.5
2.22-2.270.22961190.17352798X-RAY DIFFRACTION94.04
2.27-2.320.20731630.16622911X-RAY DIFFRACTION95.76
2.32-2.380.211520.17532810X-RAY DIFFRACTION97.27
2.38-2.440.20381390.16172890X-RAY DIFFRACTION97.77
2.44-2.510.23081390.17342987X-RAY DIFFRACTION98.36
2.51-2.60.20131520.16992904X-RAY DIFFRACTION98.39
2.6-2.690.23841560.18032903X-RAY DIFFRACTION98.27
2.69-2.80.25011530.18332888X-RAY DIFFRACTION98
2.8-2.920.23041540.18162923X-RAY DIFFRACTION98.59
2.92-3.080.24461360.17972938X-RAY DIFFRACTION98.34
3.08-3.270.2131460.16452900X-RAY DIFFRACTION97.5
3.27-3.520.17381500.14992877X-RAY DIFFRACTION97.43
3.52-3.880.18152040.13412804X-RAY DIFFRACTION96.69
3.88-4.440.14991800.11632940X-RAY DIFFRACTION98.67
4.44-5.590.14461700.12462877X-RAY DIFFRACTION98.16
5.59-47.360.18541260.15022921X-RAY DIFFRACTION97.5
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)
12.280020140660.668699534456-1.383683324011.0676545367-0.53890816762.15559536018-0.0547613086936-0.101747325277-0.08215408586050.01858177374020.00616363879011-0.02416652512490.137192878840.05586807158560.03631508268670.1308552464980.0271911510858-0.01828761850840.0692733744097-0.00855521317160.11865587588716.0577648874-36.23614432064.41924321324
21.478581739610.940513401887-0.2479067345021.362394929450.2134258135240.8245909351330.0582689021296-0.1333905791860.1730860963570.20054962216-0.08887836895520.0547785088364-0.1108329697360.0833771067390.003874568324520.2032297197560.0004203383371910.001522271370890.186228431649-0.01653764934540.17038188073520.590004825-1.5784126492412.7008445686
30.9958218470460.0163848028762-0.3390570082291.172925478540.09214023930721.60269826494-0.00758524060403-0.06254059635560.0457737848462-0.00190210726454-0.00460571738211-0.03179828412450.001879609427260.07531554145310.02044977055810.127628149175-0.00356902608937-0.02589211767390.1306813231340.001636764845520.13563014880118.807396962-13.5493588672.43047236196
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 3 through 140 )3 - 1401 - 138
22chain 'B' and (resid 141 through 270 )141 - 270139 - 268
33chain 'B' and (resid 271 through 442 )271 - 442269 - 440

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