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- PDB-6krw: Crystal Structure of AtPTP1 at 1.4 angstrom -

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Basic information

Entry
Database: PDB / ID: 6krw
TitleCrystal Structure of AtPTP1 at 1.4 angstrom
ComponentsProtein-tyrosine-phosphatase PTP1
KeywordsHYDROLASE / classical protein tyrosine phosphatase / Arabidopsis thaliana
Function / homology
Function and homology information


negative regulation of defense response / MAP kinase tyrosine phosphatase activity / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / defense response / kinase binding / intracellular signal transduction / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like
Similarity search - Domain/homology
CITRATE ANION / IODIDE ION / DI(HYDROXYETHYL)ETHER / Protein-tyrosine-phosphatase PTP1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsZhao, Y.Y. / Luo, Z.P. / Wang, J. / Wu, J.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China) China
CitationJournal: To Be Published
Title: Crystal structure of AtPTP1 at 1.4 Angstroms
Authors: Zhao, Y.Y. / Wang, H.J. / Hu, J. / Tang, J. / Zhang, W.H. / He, Q.Q. / Deng, H.T. / Luo, Z.P. / Wang, J. / Wang, Z.X. / Wang, X.L. / Wu, J.W.
History
DepositionAug 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-tyrosine-phosphatase PTP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1956
Polymers34,5191
Non-polymers6765
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint1 kcal/mol
Surface area13680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.682, 42.213, 72.959
Angle α, β, γ (deg.)90.00, 109.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein-tyrosine-phosphatase PTP1 / Protein tyrosine phosphatase 1 / AtPTP1


Mass: 34519.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PTP1, At1g71860, F14O23.24 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: O82656, protein-tyrosine-phosphatase
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M sodium citrate (pH 6.0), 25 ~ 30% polyethylene glycol (PEG) 3350, 0.2 M potassium iodide.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 65204 / % possible obs: 97.4 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.015 / Rrim(I) all: 0.04 / Net I/σ(I): 45.3
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 6439 / CC1/2: 0.848 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
HKL-2000v716data reduction
HKL-2000v716data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HNP

2hnp


Resolution: 1.4→37.5 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.948 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16611 3296 5.1 %RANDOM
Rwork0.13309 ---
obs0.13474 61902 97.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.38 Å2
Baniso -1Baniso -2Baniso -3
1--2.84 Å20 Å20.01 Å2
2---0.43 Å20 Å2
3---2.61 Å2
Refinement stepCycle: 1 / Resolution: 1.4→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2409 0 23 196 2628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132504
X-RAY DIFFRACTIONr_bond_other_d0.0060.0172279
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.643404
X-RAY DIFFRACTIONr_angle_other_deg1.11.575309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8285311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.85823.178129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.76815430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1921514
X-RAY DIFFRACTIONr_chiral_restr0.0870.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0350.022800
X-RAY DIFFRACTIONr_gen_planes_other0.0320.02494
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it14.9476.8371238
X-RAY DIFFRACTIONr_mcbond_other14.9386.8341237
X-RAY DIFFRACTIONr_mcangle_it14.87612.7491551
X-RAY DIFFRACTIONr_mcangle_other14.87712.7571552
X-RAY DIFFRACTIONr_scbond_it14.2327.7581266
X-RAY DIFFRACTIONr_scbond_other14.2277.7581267
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other15.73114.0521854
X-RAY DIFFRACTIONr_long_range_B_refined15.35765.24410893
X-RAY DIFFRACTIONr_long_range_B_other15.39565.03410742
X-RAY DIFFRACTIONr_rigid_bond_restr14.2134783
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å
RfactorNum. reflection% reflection
Rfree0.228 243 -
Rwork0.221 4467 -
obs--96.16 %

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