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- PDB-2qep: Crystal structure of the D1 domain of PTPRN2 (IA2beta) -

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Basic information

Entry
Database: PDB / ID: 2qep
TitleCrystal structure of the D1 domain of PTPRN2 (IA2beta)
ComponentsReceptor-type tyrosine-protein phosphatase N2
KeywordsHYDROLASE / PTPRN2 / PTPRP / Phogrin / IA-2 beta / autoantigen / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of secretion / transmembrane receptor protein tyrosine phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / neurotransmitter secretion / insulin secretion involved in cellular response to glucose stimulus / ficolin-1-rich granule membrane / protein dephosphorylation / protein-tyrosine-phosphatase / secretory granule membrane / secretory granule ...regulation of secretion / transmembrane receptor protein tyrosine phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / neurotransmitter secretion / insulin secretion involved in cellular response to glucose stimulus / ficolin-1-rich granule membrane / protein dephosphorylation / protein-tyrosine-phosphatase / secretory granule membrane / secretory granule / lipid metabolic process / synaptic vesicle membrane / receptor complex / synapse / Neutrophil degranulation / plasma membrane
Similarity search - Function
Protein-tyrosine phosphatase receptor IA-2 ectodomain / RESP18 domain / Receptor-type tyrosine-protein phosphatase-like N/N2 / Protein-tyrosine phosphatase receptor IA-2, ectodomain superfamily / Protein-tyrosine phosphatase receptor IA-2 / RESP18 domain / RESP18 / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain ...Protein-tyrosine phosphatase receptor IA-2 ectodomain / RESP18 domain / Receptor-type tyrosine-protein phosphatase-like N/N2 / Protein-tyrosine phosphatase receptor IA-2, ectodomain superfamily / Protein-tyrosine phosphatase receptor IA-2 / RESP18 domain / RESP18 / 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
Receptor-type tyrosine-protein phosphatase N2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsUgochukwu, E. / Barr, A. / Alfano, I. / Berridge, G. / Burgess-Brown, N. / Das, S. / Fedorov, O. / King, O. / Niesen, F. / Watt, S. ...Ugochukwu, E. / Barr, A. / Alfano, I. / Berridge, G. / Burgess-Brown, N. / Das, S. / Fedorov, O. / King, O. / Niesen, F. / Watt, S. / Savitsky, P. / Salah, E. / Pike, A.C.W. / Bunkoczi, G. / von Delft, F. / Sundstrom, M. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / 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
DepositionJun 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 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 / 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Receptor-type tyrosine-protein phosphatase N2
B: Receptor-type tyrosine-protein phosphatase N2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9903
Polymers69,9552
Non-polymers351
Water70339
1
A: Receptor-type tyrosine-protein phosphatase N2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0132
Polymers34,9771
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Receptor-type tyrosine-protein phosphatase N2


Theoretical massNumber of molelcules
Total (without water)34,9771
Polymers34,9771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.541, 136.555, 35.752
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPVALVALAA724 - 77111 - 58
21ASPASPVALVALBB724 - 77111 - 58
12SERSERASNASNAA776 - 89863 - 185
22SERSERASNASNBB776 - 89863 - 185
13VALVALVALVALAA903 - 930190 - 217
23VALVALVALVALBB903 - 930190 - 217
14GLYGLYALAALAAA936 - 976223 - 263
24GLYGLYALAALABB936 - 976223 - 263

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Components

#1: Protein Receptor-type tyrosine-protein phosphatase N2 / R-PTP-N2 / Islet cell autoantigen-related protein / ICAAR / IAR / Phogrin


Mass: 34977.453 Da / Num. of mol.: 2 / Fragment: D1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRN2 / Plasmid: pNIC-CH / Production host: Escherichia coli (E. coli)
Strain (production host): Phage-resistant derivative of BL21(DE3)
References: UniProt: Q92932, protein-tyrosine-phosphatase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.29 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Na/KPO4, 0.1 M Bis-tris-propane pH 6.5, 20.0% PEG 3350, 10.0% Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.5→59.23 Å / Num. all: 23096 / Num. obs: 23096 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.139 / Rsym value: 0.139 / Net I/σ(I): 9.1
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 1.9 / Num. unique all: 11455 / Rsym value: 0.465 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
MAR345CCDdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2I1Y

2i1y


Resolution: 2.5→59.23 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.874 / SU B: 25.532 / SU ML: 0.266 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.629 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28601 1187 5.1 %RANDOM
Rwork0.23634 ---
all0.2389 21905 --
obs0.2389 21905 99.14 %-
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: 31.042 Å2
Baniso -1Baniso -2Baniso -3
1-1.7 Å20 Å20 Å2
2---2.97 Å20 Å2
3---1.28 Å2
Refinement stepCycle: LAST / Resolution: 2.5→59.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4413 0 1 39 4453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0214522
X-RAY DIFFRACTIONr_bond_other_d0.0010.022869
X-RAY DIFFRACTIONr_angle_refined_deg1.311.9296175
X-RAY DIFFRACTIONr_angle_other_deg0.88236984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5125570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7223.951205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18315663
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5261523
X-RAY DIFFRACTIONr_chiral_restr0.0710.2695
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025131
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02936
X-RAY DIFFRACTIONr_nbd_refined0.2180.21018
X-RAY DIFFRACTIONr_nbd_other0.1880.22953
X-RAY DIFFRACTIONr_nbtor_refined0.1880.22199
X-RAY DIFFRACTIONr_nbtor_other0.0860.22280
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2116
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0160.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2640.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2910.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.22
X-RAY DIFFRACTIONr_mcbond_it0.4671.52937
X-RAY DIFFRACTIONr_mcbond_other0.091.51148
X-RAY DIFFRACTIONr_mcangle_it0.78924594
X-RAY DIFFRACTIONr_scbond_it1.06931843
X-RAY DIFFRACTIONr_scangle_it1.5564.51581
Refine LS restraints NCS

Ens-ID: 1 / Number: 3422 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.360.5
2Bmedium thermal0.332
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 100 -
Rwork0.272 1605 -
obs--99.24 %
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)
12.96190.6301-0.17561.2678-0.18811.13160.02820.1594-0.0099-0.02830.0050.11930.083-0.0961-0.0332-0.11150.0184-0.0123-0.0444-0.0297-0.095535.34065.05932.7838
21.41720.93110.27063.0110.15421.29490.0168-0.0207-0.09740.1193-0.031-0.01380.1756-0.04990.0143-0.04830.03270.04-0.02680.0167-0.12385.399937.676-2.8659
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA724 - 97411 - 261
2X-RAY DIFFRACTION2BB724 - 97411 - 261

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