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- PDB-7moj: Crystal Structure of Arabidopsis thaliana Plant and Fungi Atypica... -

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Basic information

Entry
Database: PDB / ID: 7moj
TitleCrystal Structure of Arabidopsis thaliana Plant and Fungi Atypical Dual Specificity Phosphatase 1(AtPFA-DSP1 ) Cys150Ser in complex with a metaphosphate intermediate
ComponentsTyrosine-protein phosphatase DSP1
KeywordsHYDROLASE / inositol / inositol pyrophosphate / TRANSFERASE / cell-signaling / phosphatase / substrate recognition / reaction mechanism / intermediate / phosphate / metaphosphate / molecular dynamic simulation / self-activation / catalytic water
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-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity / inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity / diphosphoinositol-polyphosphate diphosphatase / phosphatase activity / protein tyrosine phosphatase activity
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 profile. / Dual specificity protein phosphatase domain / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Protein-tyrosine phosphatase-like
Similarity search - Domain/homology
PHOSPHITE ION / Inositol diphosphatase DSP1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 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)1ZIAES080046-29 United States
CitationJournal: Nat Commun / Year: 2022
Title: A structural expose of noncanonical molecular reactivity within the protein tyrosine phosphatase WPD loop.
Authors: Wang, H. / Perera, L. / Jork, N. / Zong, G. / Riley, A.M. / Potter, B.V.L. / Jessen, H.J. / Shears, S.B.
History
DepositionMay 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase DSP1
B: Tyrosine-protein phosphatase DSP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4434
Polymers39,2862
Non-polymers1582
Water8,017445
1
A: Tyrosine-protein phosphatase DSP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7222
Polymers19,6431
Non-polymers791
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein phosphatase DSP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7222
Polymers19,6431
Non-polymers791
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.152, 125.152, 125.152
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Tyrosine-protein phosphatase DSP1 / Protein PLANT AND FUNGI ATYPICAL DUAL-SPECIFICITY PHOSPHATASE 1 / AtPFA-DSP1 / Tyrosine-protein ...Protein PLANT AND FUNGI ATYPICAL DUAL-SPECIFICITY PHOSPHATASE 1 / AtPFA-DSP1 / Tyrosine-protein phosphatase At1g05000


Mass: 19642.770 Da / Num. of mol.: 2 / Mutation: C150S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DSP1, PTP135, At1g05000, T7A14.14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ZVN4, protein-tyrosine-phosphatase
#2: Chemical ChemComp-PO3 / PHOSPHITE ION


Mass: 78.972 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 4.16 Å3/Da / Density % sol: 70.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.4 M NaCl, 100 mM HEPES pH 7.2, 50 mM beta-mercaptoethanol at 298K (3 ul of 5.5 mg/ml protein plus 1 ul of well buffer in the crystallization drop). The formed crystal was soaked in 30% ...Details: 0.4 M NaCl, 100 mM HEPES pH 7.2, 50 mM beta-mercaptoethanol at 298K (3 ul of 5.5 mg/ml protein plus 1 ul of well buffer in the crystallization drop). The formed crystal was soaked in 30% PEG400, 13mM MgCl2, 33mM NaF, 50 mM beta-mercaptoethanol, 66 mM HEPES, pH 7.2, and 5 mM 5-InsP7 for 2 days, and transferred into pH 10.0, 50 mM CHES for 1 hour.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 51688 / % possible obs: 100 % / Redundancy: 7.5 % / Rrim(I) all: 0.074 / Net I/σ(I): 27.8
Reflection shellResolution: 1.9→1.93 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2531 / Rrim(I) all: 0.871

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→37.76 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.966 / SU B: 3.563 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1478 2601 5.1 %RANDOM
Rwork0.1142 ---
obs0.1159 48867 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 201.02 Å2 / Biso mean: 26.991 Å2 / Biso min: 9.21 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.9→37.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2509 0 8 445 2962
Biso mean--31.5 54.95 -
Num. residues----308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132727
X-RAY DIFFRACTIONr_bond_other_d0.0180.0172527
X-RAY DIFFRACTIONr_angle_refined_deg1.521.6373695
X-RAY DIFFRACTIONr_angle_other_deg1.6081.5755887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1635342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15420.933150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31715484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7111522
X-RAY DIFFRACTIONr_chiral_restr0.0790.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023112
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02634
X-RAY DIFFRACTIONr_rigid_bond_restr6.93835254
LS refinement shellResolution: 1.9→1.948 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.215 192 -
Rwork0.17 3475 -
obs--97.29 %

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