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- PDB-4hti: Crystallographic structure of the membrane-proximal ectodomain of... -

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Basic information

Entry
Database: PDB / ID: 4hti
TitleCrystallographic structure of the membrane-proximal ectodomain of the human receptor-type protein-tyrosine phosphatase phogrin
ComponentsReceptor-type tyrosine-protein phosphatase N2
KeywordsHYDROLASE / phogrin / IA-2beta / protein-tyrosine phosphatase / transmembrane protein / diabetes / autoimmunity / Glycoprotein / Receptor / ferredoxin-like fold
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 / 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 N2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.954 Å
AuthorsNoguera, M.E. / Jakoncic, J. / Poskus, E. / Ermacora, M.R.
CitationJournal: J.Struct.Funct.Genom. / Year: 2015
Title: X-ray structure of the mature ectodomain of phogrin.
Authors: Noguera, M.E. / Primo, M.E. / Jakoncic, J. / Poskus, E. / Solimena, M. / Ermacora, M.R.
History
DepositionNov 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Mar 20, 2013Group: Database references
Revision 1.3Jul 24, 2013Group: Database references
Revision 1.4Mar 18, 2015Group: Database references
Revision 1.5Nov 15, 2017Group: Refinement description / Category: software
Revision 1.6Sep 20, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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


Theoretical massNumber of molelcules
Total (without water)10,8261
Polymers10,8261
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.133, 55.133, 148.391
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-617-

HOH

21A-618-

HOH

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Components

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


Mass: 10826.067 Da / Num. of mol.: 1 / Fragment: sequence database residues 502 - 599
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRN2, KIAA0387 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92932, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 3.01 Å3/Da / Density % sol: 59.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.2 M Ammonium sulfate, 30 % w/v Polyethylene glycol 4000, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9184 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 16, 2011 / Details: TOROIDAL FOCUSING MIRROR
RadiationMonochromator: SI(111) CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 10352 / Num. obs: 10352 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 40.5 % / Rmerge(I) obs: 0.06 / Χ2: 1.835 / Net I/σ(I): 14.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-1.9841.40.9935001.6351100
1.98-2.0242.40.8634951.6271100
2.02-2.0641.80.7384901.621100
2.06-2.141.70.5535131.6471100
2.1-2.1541.60.444961.6541100
2.15-2.241.90.3565131.6961100
2.2-2.2541.70.3234911.7391100
2.25-2.3141.50.245121.6291100
2.31-2.3841.60.2195121.671100
2.38-2.4641.70.1664951.6811100
2.46-2.5441.30.1335131.7021100
2.54-2.6541.20.1175201.6991100
2.65-2.7741.40.0915131.7421100
2.77-2.9141.20.0715131.9081100
2.91-3.0940.50.0585272.0531100
3.09-3.3340.70.0525132.2111100
3.33-3.6739.70.0445442.4781100
3.67-4.239.10.0395382.3581100
4.2-5.2837.20.0345542.136199.5
5.28-3032.60.0326001.792194.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QT7

2qt7


Resolution: 1.954→29.29 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2427 498 4.8 %RANDOM
Rwork0.2214 ---
obs0.2223 10292 99.45 %-
all-10352 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.65 Å2 / Biso mean: 48.3448 Å2 / Biso min: 25.28 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20.63 Å20 Å2
2--1.27 Å2-0 Å2
3----1.9 Å2
Refinement stepCycle: LAST / Resolution: 1.954→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms670 0 0 40 710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.019681
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.989925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.037589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1382530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.17715123
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.058156
X-RAY DIFFRACTIONr_chiral_restr0.1130.2114
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021504
LS refinement shellResolution: 1.954→2.005 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 31 -
Rwork0.328 692 -
all-723 -
obs--97.83 %
Refinement TLS params.Method: refined / Origin x: -8.395 Å / Origin y: -20.328 Å / Origin z: -1.975 Å
111213212223313233
T0.0294 Å20.0105 Å20.0015 Å2-0.2741 Å2-0.0543 Å2--0.0906 Å2
L7.9888 °2-1.9278 °24.0959 °2-2.3455 °2-1.6715 °2--7.8186 °2
S-0.0465 Å °-0.8414 Å °0.2788 Å °0.0717 Å °-0.1593 Å °-0.212 Å °-0.2905 Å °-0.1054 Å °0.2059 Å °

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