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

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Basic information

Entry
Database: PDB / ID: 4htj
TitleCrystallographic structure of the membrane-proximal ectodomain of the human receptor-type protein-tyrosine phosphatase phogrin at pH 4.6
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 / Neutrophil degranulation / synapse / 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: 2.011 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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

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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
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.742, 54.742, 149.147
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-624-

HOH

21A-626-

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.: 34 / 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: 2.98 Å3/Da / Density % sol: 58.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M Ammonium sulfate, 0.1 M Sodium acetate trihydrate pH 4.6, 25 % w/v Polyethylene glycol 4000, 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: 2→20 Å / Num. all: 9208 / Num. obs: 9208 / % possible obs: 95.4 % / Observed criterion σ(I): 2 / Redundancy: 12.5 % / Rmerge(I) obs: 0.063 / Χ2: 1.515 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.039.70.7912921.51161.9
2.03-2.0711.50.7044541.508199.1
2.07-2.1111.80.624771.549199.6
2.11-2.1511.80.4514571.561199.6
2.15-2.2120.3764621.616199.1
2.2-2.2512.10.3814521.626199.6
2.25-2.3112.10.2654701.593199.2
2.31-2.3712.40.2724751.686199.2
2.37-2.4412.50.2034551.675199.3
2.44-2.5212.50.1574701.644199.4
2.52-2.61130.1494761.667198.8
2.61-2.7113.10.1224601.629198.3
2.71-2.8413.10.0974691.584198.7
2.84-2.9913.30.0774751.562198.1
2.99-3.1713.70.0624791.552198.2
3.17-3.4213.70.0494771.394197.3
3.42-3.7613.70.0434691.274196.7
3.76-4.313.30.044851.235195.1
4.3-5.3912.80.0384781.161192.1
5.39-2011.40.0424761.332181.9

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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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QT7

2qt7


Resolution: 2.011→18.4 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2377 440 4.8 %RANDOM
Rwork0.2025 ---
obs0.204 9206 97.46 %-
all-9208 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.18 Å2 / Biso mean: 46.7844 Å2 / Biso min: 29.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0.11 Å2-0 Å2
2---0.23 Å2-0 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.011→18.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms676 0 0 34 710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.019692
X-RAY DIFFRACTIONr_angle_refined_deg21.989939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.144590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.52225.16131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1315125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.078156
X-RAY DIFFRACTIONr_chiral_restr0.1250.2114
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021516
LS refinement shellResolution: 2.011→2.062 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 27 -
Rwork0.277 621 -
all-648 -
obs--98.48 %
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)
114.2234.09012.67331.190.46247.95340.0485-0.0824-0.60050.0042-0.0473-0.17470.51220.1201-0.00110.4371-0.00290.0070.38920.02640.1145-9.508-25.854-6.155
28.9144-2.62871.46196.5098-3.786417.3176-0.25790.02980.63780.0846-0.46-0.1423-0.94640.27960.7180.4298-0.0127-0.06650.33510.03170.1558-13.496-13.208-12.091
350.47014.180810.43550.90795.83946.2507-0.69312.16972.0061-0.28730.32090.1641-2.24931.62910.37220.5086-0.071-0.07230.38890.16290.2031-5.259-12.644-12.319
48.1456-1.088-0.77515.44077.398731.25160.01160.20730.36110.19110.4013-0.52820.10011.6727-0.4130.39190.0345-0.11520.4454-0.05110.2105-2.75-14.687-3.438
523.5626-18.963617.235516.4248-10.05829.2804-0.266-0.613-0.01750.03230.20920.2976-0.1704-0.630.05680.44510.0328-0.16580.4596-0.11990.3073-2.021-17.9246.14
632.7426-2.523214.633817.244414.328420.555-0.09750.07880.6886-0.27730.158-0.4716-0.30620.1596-0.06050.3701-0.0225-0.02770.3870.03550.12443.004-22.163-0.435
729.7294-5.760419.08868.1348-3.564220.84170.73320.8908-1.3671-0.02280.09990.03910.55031.0641-0.83320.30890.0145-0.00270.37750.00310.0878-4.017-22.368-11.967
824.9139-7.227514.48442.3595-3.308311.55080.4666-0.0541-0.3068-0.068300.02450.3997-0.1371-0.46670.3786-0.0117-0.03470.3577-0.00260.1177-5.732-24.012-6.807
914.8247-5.1087-0.844712.31415.012816.8799-0.1375-0.4131-1.0470.39150.36980.55050.3822-0.1486-0.23240.32920.0035-0.01410.3220.08630.10941.607-28.2396.586
1049.13283.899427.34091.2653-3.47648.67730.32380.1491-2.6538-0.38290.3497-0.35832.5441-1.6981-0.67340.5842-0.17330.07880.5915-0.10750.338-8.35-27.6752.946
1115.8226-1.48351.935723.708818.383514.8799-0.2471-1.3882-0.82421.27870.19680.24250.8849-0.20650.05030.56980.1470.00360.84660.01450.1335-12.543-21.2285.996
1223.2142-1.79877.415516.0959-5.323928.9032-0.7194-2.36630.87391.31370.32850.1923-0.9327-1.1190.39080.40120.1542-0.04210.542-0.18480.0779-13.457-11.9353.372
1323.028-2.37938.270816.82095.83269.0275-0.6155-0.82591.06780.1323-0.0224-0.0364-0.8497-0.59970.6380.61520.0533-0.1150.3789-0.09780.1186-12.975-11.361-2.686
143.7411-6.1515-0.192617.6570.69285.30840.08780.3394-0.10330.505-0.3977-0.02720.60240.03770.30990.3875-0.00550.030.397-0.01670.0863-13.094-29.249-6.583
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A510 - 515
2X-RAY DIFFRACTION2A516 - 520
3X-RAY DIFFRACTION3A521 - 525
4X-RAY DIFFRACTION4A526 - 532
5X-RAY DIFFRACTION5A533 - 539
6X-RAY DIFFRACTION6A540 - 545
7X-RAY DIFFRACTION7A546 - 551
8X-RAY DIFFRACTION8A552 - 558
9X-RAY DIFFRACTION9A559 - 566
10X-RAY DIFFRACTION10A567 - 571
11X-RAY DIFFRACTION11A572 - 577
12X-RAY DIFFRACTION12A578 - 583
13X-RAY DIFFRACTION13A584 - 589
14X-RAY DIFFRACTION14A590 - 598

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