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- PDB-6krx: Crystal Structure of AtPTP1 at 1.7 angstrom -

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Basic information

Entry
Database: PDB / ID: 6krx
TitleCrystal Structure of AtPTP1 at 1.7 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 / Protein-tyrosine-phosphatase PTP1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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: AtPTP1 positively mediates brassinosteroid signaling from receptor kinases to GSK3-like kinase BIN2
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)38,2824
Polymers37,8391
Non-polymers4433
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint1 kcal/mol
Surface area13600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.536, 38.970, 75.525
Angle α, β, γ (deg.)90.000, 110.815, 90.000
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: 37838.797 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.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.12 Å3/Da / Density % sol: 41.93 %
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 PILATUS 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: 1.7→50 Å / Num. obs: 34099 / % possible obs: 96.6 % / Redundancy: 4.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.021 / Rrim(I) all: 0.049 / Net I/σ(I): 30.4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 6 / Num. unique obs: 2732 / CC1/2: 0.951 / Rpim(I) all: 0.106 / Rrim(I) all: 0.22 / % possible all: 78.4

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Processing

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

2hnp


Resolution: 1.7→37.201 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.539 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.088
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1743 1713 5.026 %Random selection
Rwork0.1511 ---
all0.152 ---
obs-34081 96.465 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.394 Å2
Baniso -1Baniso -2Baniso -3
1-0.138 Å20 Å20.088 Å2
2---0.251 Å20 Å2
3---0.035 Å2
Refinement stepCycle: LAST / Resolution: 1.7→37.201 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2391 0 15 216 2622
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132517
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172298
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.6413428
X-RAY DIFFRACTIONr_angle_other_deg0.3391.5715358
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1055315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.1122.977131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.81115441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9331515
X-RAY DIFFRACTIONr_chiral_restr0.0570.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0560.022834
X-RAY DIFFRACTIONr_gen_planes_other0.0520.02503
X-RAY DIFFRACTIONr_nbd_refined0.2110.2500
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1630.22230
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21256
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.21105
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2142
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1070.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1360.215
X-RAY DIFFRACTIONr_nbd_other0.1660.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1540.214
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0870.21
X-RAY DIFFRACTIONr_mcbond_it2.3343.0241242
X-RAY DIFFRACTIONr_mcbond_other2.3283.0211241
X-RAY DIFFRACTIONr_mcangle_it3.5545.6571563
X-RAY DIFFRACTIONr_mcangle_other3.5565.661564
X-RAY DIFFRACTIONr_scbond_it3.2923.7151275
X-RAY DIFFRACTIONr_scbond_other3.293.7141274
X-RAY DIFFRACTIONr_scangle_it5.0416.6151865
X-RAY DIFFRACTIONr_scangle_other5.046.6151866
X-RAY DIFFRACTIONr_lrange_it6.35731.95910915
X-RAY DIFFRACTIONr_lrange_other6.27131.6910783
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7430.198820.1821815X-RAY DIFFRACTION74.9802
1.743-1.790.1981110.1632159X-RAY DIFFRACTION90.1151
1.79-1.8420.1731280.152332X-RAY DIFFRACTION99.3939
1.842-1.8990.1641230.1492231X-RAY DIFFRACTION99.4088
1.899-1.9610.1751310.1542164X-RAY DIFFRACTION98.5401
1.961-2.0290.1711170.1472097X-RAY DIFFRACTION99.1047
2.029-2.1060.1791200.1481979X-RAY DIFFRACTION96.9963
2.106-2.1920.1481310.1361952X-RAY DIFFRACTION99.5222
2.192-2.2890.192910.1431908X-RAY DIFFRACTION99.2552
2.289-2.40.186860.1361775X-RAY DIFFRACTION99.2004
2.4-2.5290.1651050.1351682X-RAY DIFFRACTION98.0252
2.529-2.6820.179910.1381634X-RAY DIFFRACTION99.0241
2.682-2.8660.186700.1461537X-RAY DIFFRACTION99.2588
2.866-3.0940.165630.1481457X-RAY DIFFRACTION99.0228
3.094-3.3870.177630.151311X-RAY DIFFRACTION98.213
3.387-3.7830.186520.1581217X-RAY DIFFRACTION98.986
3.783-4.360.159570.1521068X-RAY DIFFRACTION98.8577
4.36-5.3220.167430.149896X-RAY DIFFRACTION97.8125
5.322-7.4510.169290.212729X-RAY DIFFRACTION98.6979
7.451-37.2010.193200.183425X-RAY DIFFRACTION96.9499

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