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- PDB-4ge2: Crystal structure of human protein tyrosine phosphatase PTPN9 (ME... -

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Basic information

Entry
Database: PDB / ID: 4ge2
TitleCrystal structure of human protein tyrosine phosphatase PTPN9 (MEG2) complex with compound 3
ComponentsTyrosine-protein phosphatase non-receptor type 9
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


neuron projection terminus / Interleukin-37 signaling / non-membrane spanning protein tyrosine phosphatase activity / peptidyl-tyrosine dephosphorylation / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / positive regulation of protein localization to plasma membrane / negative regulation of neuron projection development / nucleoplasm / cytoplasm
Similarity search - Function
CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / : / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Protein tyrosine phosphatase superfamily ...CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / : / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-75A / Tyrosine-protein phosphatase non-receptor type 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsZhang, Z.-Y. / Liu, S. / Zhang, S.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: A Highly Selective and Potent PTP-MEG2 Inhibitor with Therapeutic Potential for Type 2 Diabetes.
Authors: Zhang, S. / Liu, S. / Tao, R. / Wei, D. / Chen, L. / Shen, W. / Yu, Z.H. / Wang, L. / Jones, D.R. / Dong, X.C. / Zhang, Z.Y.
History
DepositionAug 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 9
B: Tyrosine-protein phosphatase non-receptor type 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1383
Polymers72,4582
Non-polymers6801
Water7,278404
1
A: Tyrosine-protein phosphatase non-receptor type 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9092
Polymers36,2291
Non-polymers6801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosine-protein phosphatase non-receptor type 9


Theoretical massNumber of molelcules
Total (without water)36,2291
Polymers36,2291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.982, 57.747, 66.544
Angle α, β, γ (deg.)77.33, 78.28, 80.27
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 9 / Protein-tyrosine phosphatase MEG2 / PTPase MEG2


Mass: 36229.055 Da / Num. of mol.: 2
Fragment: tyrosine-protein phosphatase domain (UNP residues 277-582)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN9 / Plasmid: PNIC-CH / Production host: Escherichia coli (E. coli)
Strain (production host): phage-resistant derivative of BL21(DE3)
References: UniProt: P43378, protein-tyrosine-phosphatase
#2: Chemical ChemComp-75A / N-acetyl-4-[difluoro(phosphono)methyl]-L-phenylalanyl-N~5~-(3-iodobenzoyl)-L-ornithinamide


Type: peptide-like / Mass: 680.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H28F2IN4O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.01 Å3/Da / Density % sol: 38.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 25% PEG3350, 0.2 M potassium thiocyanate, 10% ethylene glycol, 0.1 M Bis-Tris propane, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM
DetectorType: ADSC QUANTUM 210r / Detector: CCD
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.24→50 Å / Num. obs: 105301 / % possible obs: 68.6 % / Observed criterion σ(I): 1 / Redundancy: 1.8 % / Rmerge(I) obs: 0.147

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT3.11data extraction
APEXdata collection
HKL-3000data reduction
HKL-3000data scaling
AMoREphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2PA5

2pa5


Resolution: 1.8→50 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 1469 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2247 1777 3.4 %RANDOM
Rwork0.1885 42263 --
all-52231 --
obs-44040 84.3 %-
Solvent computationBsol: 44.9849 Å2
Displacement parametersBiso max: 42.54 Å2 / Biso mean: 22.7285 Å2 / Biso min: 3.79 Å2
Baniso -1Baniso -2Baniso -3
1--1.392 Å20.482 Å2-0.067 Å2
2---0.945 Å2-0.201 Å2
3---2.336 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4815 0 39 404 5258
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.149
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3A75_par.txt
X-RAY DIFFRACTION4CNS_TOPPAR:water.param

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