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- PDB-7qwj: Crystal structure of Glc7 phosphatase -

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Basic information

Entry
Database: PDB / ID: 7qwj
TitleCrystal structure of Glc7 phosphatase
ComponentsSerine/threonine-protein phosphatase PP1-2
KeywordsTRANSLATION / phosphatase / translation initiation / stress response
Function / homology
Function and homology information


regulation of cell budding / regulation of protein localization to cell division site involved in cytokinesis / mating projection base / cellular bud neck septin collar / : / positive regulation of mitotic actomyosin contractile ring assembly / regulation of cellular response to glucose starvation / : / : / : ...regulation of cell budding / regulation of protein localization to cell division site involved in cytokinesis / mating projection base / cellular bud neck septin collar / : / positive regulation of mitotic actomyosin contractile ring assembly / regulation of cellular response to glucose starvation / : / : / : / positive regulation of clathrin-dependent endocytosis / termination of RNA polymerase II transcription, poly(A)-coupled / protein phosphatase type 1 complex / ascospore formation / cellular bud site selection / regulation of glycogen biosynthetic process / regulation of glycogen metabolic process / incipient cellular bud site / mRNA cleavage and polyadenylation specificity factor complex / intracellular monoatomic ion homeostasis / negative regulation of actin filament polymerization / DNA replication checkpoint signaling / cellular bud neck / protein localization to kinetochore / spindle pole body / myosin phosphatase activity / protein serine/threonine phosphatase activity / glycogen metabolic process / mitotic spindle assembly checkpoint signaling / protein-serine/threonine phosphatase / replication fork processing / cell division site / response to unfolded protein / chromosome organization / regulation of mitotic cell cycle / telomere maintenance / DNA damage checkpoint signaling / meiotic cell cycle / chromosome segregation / kinetochore / regulation of cell shape / response to heat / regulation of cell cycle / nucleolus / positive regulation of transcription by RNA polymerase II / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Serine/threonine-protein phosphatase PP1-gamma catalytic subunit / Serine-threonine protein phosphatase, N-terminal / Serine-threonine protein phosphatase N-terminal domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
: / PHOSPHATE ION / Serine/threonine-protein phosphatase PP1-2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMalhotra, K. / Carminati, M. / Bertolotti, A. / Bellini, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust206367/Z/17/Z United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of Glc7 phosphatase
Authors: Bellini, D. / Malhotra, K. / Carminati, M. / Bertolotti, A.
History
DepositionJan 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: 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: Serine/threonine-protein phosphatase PP1-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1814
Polymers35,9761
Non-polymers2053
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-20 kcal/mol
Surface area12960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.284, 83.294, 96.532
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Serine/threonine-protein phosphatase PP1-2


Mass: 35976.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GLC7, CID1, DIS2, YER133W / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P32598, protein-serine/threonine phosphatase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.14 Å3/Da / Density % sol: 42.43 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 4,000, 200 mM MgCl2 and 100 mM TrisHCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→63.063 Å / Num. obs: 22215 / % possible obs: 94.2 % / Redundancy: 12.9 % / CC1/2: 1 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.02 / Rrim(I) all: 0.074 / Net I/σ(I): 19.7
Reflection shellResolution: 1.65→1.879 Å / Rmerge(I) obs: 1.034 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1112 / CC1/2: 0.741 / Rpim(I) all: 0.357 / Rrim(I) all: 0.939

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MOV

4mov


Resolution: 1.65→48.27 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2665 1127 5.07 %
Rwork0.2193 21084 -
obs0.2216 22211 58.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.38 Å2 / Biso mean: 31.2192 Å2 / Biso min: 13.26 Å2
Refinement stepCycle: final / Resolution: 1.65→48.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2409 0 7 84 2500
Biso mean--21.72 32.46 -
Num. residues----298
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.65-1.730.29688129
1.73-1.820.3956310.3329462
1.82-1.930.3652470.30296822
1.93-2.080.28391050.2855194544
2.08-2.290.29352160.2775376484
2.29-2.620.30232460.26454495100
2.62-3.30.29012410.2424542100
3.3-3.80.2282330.17384779100

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