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- PDB-6byf: Crystal structure of the core catalytic domain of PP-IP phosphata... -

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Basic information

Entry
Database: PDB / ID: 6byf
TitleCrystal structure of the core catalytic domain of PP-IP phosphatase SIW14 from S. cerevisiae in complex with citrate
ComponentsTyrosine-protein phosphatase SIW14
KeywordsTRANSFERASE / protein tyrosine phosphatase / phosphatase / inositol / inositol polyphosphate / inositol pyrophosphate / substrate specificity
Function / homology
Function and homology information


inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity / inositol-5-diphosphate-1,3,4,6-tetrakisphosphate diphosphatase activity / inositol diphosphate tetrakisphosphate diphosphatase activity / inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity / : / diphosphoinositol-polyphosphate diphosphatase / diphosphoinositol-polyphosphate diphosphatase activity / protein tyrosine/serine/threonine phosphatase activity / phosphatase activity / protein dephosphorylation ...inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity / inositol-5-diphosphate-1,3,4,6-tetrakisphosphate diphosphatase activity / inositol diphosphate tetrakisphosphate diphosphatase activity / inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity / : / diphosphoinositol-polyphosphate diphosphatase / diphosphoinositol-polyphosphate diphosphatase activity / protein tyrosine/serine/threonine phosphatase activity / phosphatase activity / protein dephosphorylation / actin filament organization / cytoplasm / cytosol
Similarity search - Function
Atypical dual-specificity phosphatase Siw14-like, plant and fungi / Atypical dual-specificity phosphatase Siw14-like / Tyrosine phosphatase family / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Protein-tyrosine phosphatase-like ...Atypical dual-specificity phosphatase Siw14-like, plant and fungi / Atypical dual-specificity phosphatase Siw14-like / Tyrosine phosphatase family / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Inositol phosphatase SIW14
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsWang, H. / Shears, S.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural and biochemical characterization of Siw14: A protein-tyrosine phosphatase fold that metabolizes inositol pyrophosphates.
Authors: Wang, H. / Gu, C. / Rolfes, R.J. / Jessen, H.J. / Shears, S.B.
History
DepositionDec 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Mar 16, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase SIW14
B: Tyrosine-protein phosphatase SIW14
C: Tyrosine-protein phosphatase SIW14
D: Tyrosine-protein phosphatase SIW14
E: Tyrosine-protein phosphatase SIW14
F: Tyrosine-protein phosphatase SIW14
G: Tyrosine-protein phosphatase SIW14
H: Tyrosine-protein phosphatase SIW14
I: Tyrosine-protein phosphatase SIW14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,40723
Polymers179,4209
Non-polymers1,98614
Water7,422412
1
A: Tyrosine-protein phosphatase SIW14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1903
Polymers19,9361
Non-polymers2542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein phosphatase SIW14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1282
Polymers19,9361
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tyrosine-protein phosphatase SIW14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1903
Polymers19,9361
Non-polymers2542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tyrosine-protein phosphatase SIW14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2254
Polymers19,9361
Non-polymers2903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Tyrosine-protein phosphatase SIW14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1282
Polymers19,9361
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Tyrosine-protein phosphatase SIW14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1282
Polymers19,9361
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Tyrosine-protein phosphatase SIW14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1633
Polymers19,9361
Non-polymers2282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Tyrosine-protein phosphatase SIW14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1282
Polymers19,9361
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Tyrosine-protein phosphatase SIW14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1282
Polymers19,9361
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.968, 92.968, 814.716
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11I-426-

HOH

21I-432-

HOH

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Components

#1: Protein
Tyrosine-protein phosphatase SIW14


Mass: 19935.592 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SIW14, YNL032W, N2746 / Production host: Escherichia coli (E. coli) / References: UniProt: P53965, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / Source method: isolated from a natural source / Formula: H2O

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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: 2.9 Å3/Da / Density % sol: 57.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.7M sodium citrate, 50 mM ?-mercaptoethanol / PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97177 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 15, 2016
RadiationMonochromator: Rosenbaum-Rock vertical focusing mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97177 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. obs: 162303 / % possible obs: 97.9 % / Redundancy: 5.2 % / Rrim(I) all: 0.116 / Χ2: 0.831 / Net I/σ(I): 15.1
Reflection shellResolution: 2.34→2.38 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 7262 / CC1/2: 0.824 / Rrim(I) all: 0.544 / Χ2: 0.552 / % possible all: 87.1

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→49.454 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.56
RfactorNum. reflection% reflection
Rfree0.2285 3595 2.23 %
Rwork0.2059 --
obs0.2064 160875 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.35→49.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12258 0 14 412 12684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512566
X-RAY DIFFRACTIONf_angle_d0.79516988
X-RAY DIFFRACTIONf_dihedral_angle_d20.2574778
X-RAY DIFFRACTIONf_chiral_restr0.0521822
X-RAY DIFFRACTIONf_plane_restr0.0042186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.38090.32621240.27635507X-RAY DIFFRACTION88
2.3809-2.41350.31261270.27295772X-RAY DIFFRACTION94
2.4135-2.4480.28851440.25516239X-RAY DIFFRACTION100
2.448-2.48460.29891410.25126104X-RAY DIFFRACTION100
2.4846-2.52340.27061410.25096182X-RAY DIFFRACTION100
2.5234-2.56470.29061370.24736152X-RAY DIFFRACTION100
2.5647-2.6090.29991420.2486119X-RAY DIFFRACTION100
2.609-2.65640.31771420.23716258X-RAY DIFFRACTION100
2.6564-2.70750.27131390.24736083X-RAY DIFFRACTION100
2.7075-2.76280.28741450.25026191X-RAY DIFFRACTION100
2.7628-2.82280.29611330.23786255X-RAY DIFFRACTION100
2.8228-2.88850.28821420.23226136X-RAY DIFFRACTION100
2.8885-2.96070.28181430.23126131X-RAY DIFFRACTION100
2.9607-3.04080.28211450.22786166X-RAY DIFFRACTION100
3.0408-3.13020.24681400.22556146X-RAY DIFFRACTION100
3.1302-3.23120.23811410.21896176X-RAY DIFFRACTION100
3.2312-3.34670.24871440.22076169X-RAY DIFFRACTION100
3.3467-3.48070.24061400.21816130X-RAY DIFFRACTION100
3.4807-3.6390.21541400.19656138X-RAY DIFFRACTION100
3.639-3.83080.23691410.18556147X-RAY DIFFRACTION99
3.8308-4.07070.16881360.17545890X-RAY DIFFRACTION96
4.0707-4.38480.18321300.17135926X-RAY DIFFRACTION96
4.3848-4.82580.16091260.1515610X-RAY DIFFRACTION91
4.8258-5.52330.18831450.17695848X-RAY DIFFRACTION95
5.5233-6.95570.1871390.20916056X-RAY DIFFRACTION98
6.9557-49.46530.19161280.1885749X-RAY DIFFRACTION93

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