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- PDB-2qt7: Crystallographic structure of the mature ectodomain of the human ... -

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Basic information

Entry
Database: PDB / ID: 2qt7
TitleCrystallographic structure of the mature ectodomain of the human receptor-type protein-tyrosine phosphatase IA-2 at 1.30 Angstroms
ComponentsReceptor-type tyrosine-protein phosphatase-like N
KeywordsHYDROLASE / IA-2 / ICA-512 / protein-tyrosine phosphatase / transmembrane protein / diabetes / autoimmunity / proteolysis / Glycoprotein / Receptor
Function / homology
Function and homology information


dense core granule maturation / positive regulation of type B pancreatic cell proliferation / regulation of secretion / luteinization / insulin secretion involved in cellular response to glucose stimulus / insulin secretion / spectrin binding / transport vesicle membrane / transcription factor binding / ubiquitin-like protein ligase binding ...dense core granule maturation / positive regulation of type B pancreatic cell proliferation / regulation of secretion / luteinization / insulin secretion involved in cellular response to glucose stimulus / insulin secretion / spectrin binding / transport vesicle membrane / transcription factor binding / ubiquitin-like protein ligase binding / axon terminus / secretory granule / response to reactive oxygen species / perikaryon / endosome / neuronal cell body / synapse / Golgi apparatus / positive regulation of transcription by RNA polymerase II / nucleus / plasma membrane
Similarity search - Function
Protein-tyrosine phosphatase receptor IA-2 ectodomain / 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, catalytic domain / PTP type protein phosphatase domain profile. ...Protein-tyrosine phosphatase receptor IA-2 ectodomain / 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, 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 Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase-like N
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsPrimo, M.E. / Klinke, S. / Sica, M.P. / Goldbaum, F.A. / Jakoncic, J. / Poskus, E. / Ermacora, M.R.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structure of the Mature Ectodomain of the Human Receptor-type Protein-tyrosine Phosphatase IA-2
Authors: Primo, M.E. / Klinke, S. / Sica, M.P. / Goldbaum, F.A. / Jakoncic, J. / Poskus, E. / Ermacora, M.R.
History
DepositionAug 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)19,7965
Polymers19,6762
Non-polymers1203
Water3,171176
1
A: Receptor-type tyrosine-protein phosphatase-like N
B: Receptor-type tyrosine-protein phosphatase-like N
hetero molecules

A: Receptor-type tyrosine-protein phosphatase-like N
B: Receptor-type tyrosine-protein phosphatase-like N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,59310
Polymers39,3524
Non-polymers2406
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x+1/2,-y,z+1/21
Buried area1330 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.756, 66.799, 73.131
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Receptor-type tyrosine-protein phosphatase-like N / R-PTP-N / PTP IA-2 / Islet cell antigen 512 / ICA 512 / Islet cell autoantigen 3


Mass: 9838.106 Da / Num. of mol.: 2 / Fragment: sequence database residues 468-558
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRN, ICA3, ICA512 / Plasmid: pET9b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q16849, protein-tyrosine-phosphatase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 1.97 Å3/Da / Density % sol: 37.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% (w/v) PEG 4000, 0.1 M Tris pH 8.5, 0.2 M CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9793, 1.5895
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 16, 2006 / Details: Toroidal focusing mirror
RadiationMonochromator: Si (111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
21.58951
ReflectionResolution: 1.3→24 Å / Num. all: 38269 / Num. obs: 38269 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.03 / Rsym value: 0.03 / Net I/σ(I): 43.1
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 5.5 / Num. unique all: 1587 / Rsym value: 0.213 / % possible all: 81.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-Ice(Blue-Ice like)data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→23.97 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.94 / SU B: 0.937 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.067 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24216 1922 5 %RANDOM
Rwork0.22048 ---
obs0.22159 36265 97.66 %-
all-38269 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.782 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20 Å2
2--0 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.3→23.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1383 0 3 176 1562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221408
X-RAY DIFFRACTIONr_angle_refined_deg1.1611.9691927
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.375195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.00125.78957
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.00115240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.521155
X-RAY DIFFRACTIONr_chiral_restr0.080.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021047
X-RAY DIFFRACTIONr_nbd_refined0.2140.2679
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21045
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2118
X-RAY DIFFRACTIONr_metal_ion_refined0.0990.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.228
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.040.22
X-RAY DIFFRACTIONr_mcbond_it0.8841.5937
X-RAY DIFFRACTIONr_mcangle_it1.47921479
X-RAY DIFFRACTIONr_scbond_it2.0013508
X-RAY DIFFRACTIONr_scangle_it3.0014.5441
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 129 -
Rwork0.267 2238 -
obs--82.99 %

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