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- PDB-2pa5: Crystal structure of human protein tyrosine phosphatase PTPN9 -

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Basic information

Entry
Database: PDB / ID: 2pa5
TitleCrystal structure of human protein tyrosine phosphatase PTPN9
ComponentsTyrosine-protein phosphatase non-receptor type 9
KeywordsHYDROLASE / Protein tyrosine phosphatase / MEG2 / PTPN9 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


neuron projection terminus / Interleukin-37 signaling / peptidyl-tyrosine dephosphorylation / non-membrane spanning protein tyrosine phosphatase activity / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / positive regulation of protein localization to plasma membrane / negative regulation of neuron projection development / signal transduction ...neuron projection terminus / Interleukin-37 signaling / peptidyl-tyrosine dephosphorylation / non-membrane spanning protein tyrosine phosphatase activity / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / positive regulation of protein localization to plasma membrane / negative regulation of neuron projection development / signal transduction / 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 profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
THIOCYANATE ION / Tyrosine-protein phosphatase non-receptor type 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsUgochukwu, E. / Barr, A. / Pike, A.C.W. / Savitsky, P. / Papagrigoriou, E. / Turnbull, A. / Uppenberg, J. / Bunkoczi, G. / Salah, E. / Das, S. ...Ugochukwu, E. / Barr, A. / Pike, A.C.W. / Savitsky, P. / Papagrigoriou, E. / Turnbull, A. / Uppenberg, J. / Bunkoczi, G. / Salah, E. / Das, S. / von Delft, F. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: Large-scale structural analysis of the classical human protein tyrosine phosphatome.
Authors: Barr, A.J. / Ugochukwu, E. / Lee, W.H. / King, O.N. / Filippakopoulos, P. / Alfano, I. / Savitsky, P. / Burgess-Brown, N.A. / Muller, S. / Knapp, S.
History
DepositionMar 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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)72,96812
Polymers72,4582
Non-polymers51010
Water7,296405
1
A: Tyrosine-protein phosphatase non-receptor type 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5187
Polymers36,2291
Non-polymers2896
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein phosphatase non-receptor type 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4515
Polymers36,2291
Non-polymers2224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.965, 57.427, 66.446
Angle α, β, γ (deg.)77.44, 78.22, 80.41
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 5 / Auth seq-ID: 278 - 306 / Label seq-ID: 3 - 31

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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: PTPN9: Tyrosine-protein phosphatase domain
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 1.99 Å3/Da / Density % sol: 38.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.15
Details: 25% PEG 3350, 0.2 M Potassium thiocyanate, 10% Ethylene glycol, 0.1 M Bis-Tris propane pH 6.15, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.6→33.96 Å / Num. all: 71616 / Num. obs: 71616 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 9
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 2.1 / Num. unique all: 19981 / Rsym value: 0.379 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2HNQ

2hnq


Resolution: 1.6→33.96 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.189 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18792 3602 5 %RANDOM
Rwork0.15559 ---
all0.15726 68013 --
obs0.15726 68013 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å2-0.14 Å20 Å2
2--0.07 Å20.13 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.6→33.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4637 0 27 405 5069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224794
X-RAY DIFFRACTIONr_bond_other_d0.0010.023264
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9416474
X-RAY DIFFRACTIONr_angle_other_deg1.15337931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5785580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.27823.778225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.35415814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8431531
X-RAY DIFFRACTIONr_chiral_restr0.090.2715
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025282
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021001
X-RAY DIFFRACTIONr_nbd_refined0.2250.2948
X-RAY DIFFRACTIONr_nbd_other0.20.23286
X-RAY DIFFRACTIONr_nbtor_refined0.1840.22409
X-RAY DIFFRACTIONr_nbtor_other0.0880.22398
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2307
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2390.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.227
X-RAY DIFFRACTIONr_mcbond_it3.05552924
X-RAY DIFFRACTIONr_mcbond_other1.89851188
X-RAY DIFFRACTIONr_mcangle_it4.26474733
X-RAY DIFFRACTIONr_scbond_it5.98591870
X-RAY DIFFRACTIONr_scangle_it8.173111741
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1681medium positional0.310.5
1994loose positional0.65
1681medium thermal1.782
1994loose thermal3.1310
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 265 -
Rwork0.209 4937 -
obs--95.07 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4577-0.1048-0.0190.6799-0.02830.5482-0.00160.03490.0108-0.05450.00360.00760.00260.0184-0.002-0.0468-0.0038-0.0029-0.04-0.0015-0.043556.19159.763662.4847
20.6307-0.3206-0.18150.64250.19320.5125-0.001-0.1018-0.08610.0658-0.02360.0026-0.0201-0.00840.0245-0.0306-0.01-0.00550.00280.0104-0.029669.468445.332792.5664
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA278 - 5813 - 306
2X-RAY DIFFRACTION2BB278 - 5783 - 303

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