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- PDB-2jjd: Protein Tyrosine Phosphatase, Receptor Type, E isoform -

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Basic information

Entry
Database: PDB / ID: 2jjd
TitleProtein Tyrosine Phosphatase, Receptor Type, E isoform
ComponentsRECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE EPSILON
KeywordsHYDROLASE / TRANSMEMBRANE / PHOSPHOPROTEIN / PROTEIN PHOSPHATASE / CONSORTIUM / STRUCTURAL / PHOSPHATASE / GLYCOPROTEIN / SGC / PTPRE / MEMBRANE / GENOMICS
Function / homology
Function and homology information


transmembrane receptor protein tyrosine phosphatase activity / negative regulation of insulin receptor signaling pathway / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Receptor tyrosine-protein phosphatase, alpha/epsilon-type / : / 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 ...Receptor tyrosine-protein phosphatase, alpha/epsilon-type / : / 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 epsilon
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsElkins, J.M. / Ugochukwu, E. / Alfano, I. / Barr, A.J. / Bunkoczi, G. / King, O.N.F. / Filippakopoulos, P. / Savitsky, P. / Salah, E. / Pike, A. ...Elkins, J.M. / Ugochukwu, E. / Alfano, I. / Barr, A.J. / Bunkoczi, G. / King, O.N.F. / Filippakopoulos, P. / Savitsky, P. / Salah, E. / Pike, A. / Johansson, C. / Das, S. / Burgess-Brown, N.A. / Gileadi, O. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Knapp, S.
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.F. / Filippakopoulos, P. / Alfano, I. / Savitsky, P. / Burgess-Brown, N.A. / Muller, S. / Knapp, S.
History
DepositionMar 31, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jun 6, 2012Group: Other
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _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

Downloads & links

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Assembly

Deposited unit
A: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE EPSILON
B: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE EPSILON
C: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE EPSILON
D: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE EPSILON
E: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE EPSILON
F: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE EPSILON
hetero molecules


Theoretical massNumber of molelcules
Total (without water)418,02818
Polymers417,6026
Non-polymers42512
Water00
1
A: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE EPSILON
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6713
Polymers69,6001
Non-polymers712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE EPSILON
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7074
Polymers69,6001
Non-polymers1063
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE EPSILON
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6362
Polymers69,6001
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE EPSILON
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6713
Polymers69,6001
Non-polymers712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE EPSILON
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6713
Polymers69,6001
Non-polymers712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE EPSILON
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6713
Polymers69,6001
Non-polymers712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.020, 123.616, 219.116
Angle α, β, γ (deg.)90.00, 91.13, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12A
22B
32C
42D
52E
62F
13A
23B
33C
43D
53E
63F
14A
24B
34C
44D
54E
64F
15A
25B
35C
45D
55E
65F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A111 - 142
2111B111 - 142
3111C111 - 142
4111D111 - 142
5111E111 - 142
6111F111 - 142
1121A152 - 235
2121B152 - 235
3121C152 - 235
4121D152 - 235
5121E152 - 235
6121F152 - 235
1221A242 - 303
2221B242 - 303
3221C242 - 303
4221D242 - 303
5221E242 - 303
6221F242 - 303
1321A313 - 359
2321B313 - 359
3321C313 - 359
4321D313 - 359
5321E313 - 359
6321F313 - 359
1421A366 - 373
2421B366 - 373
3421C366 - 373
4421D366 - 373
5421E366 - 373
6421F366 - 373
1521A387 - 423
2521B387 - 423
3521C387 - 423
4521D387 - 423
5521E387 - 423
6521F387 - 423
1134A143 - 151
2134B143 - 151
3134C143 - 151
4134D143 - 151
5134E143 - 151
6134F143 - 151
1234A236 - 241
2234B236 - 241
3234C236 - 241
4234D236 - 241
5234E236 - 241
6234F236 - 241
1334A304 - 312
2334B304 - 312
3334C304 - 312
4334D304 - 312
5334E304 - 312
6334F304 - 312
1434A360 - 365
2434B360 - 365
3434C360 - 365
4434D360 - 365
5434E360 - 365
6434F360 - 365
1534A374 - 386
2534B374 - 386
3534C374 - 386
4534D374 - 386
5534E374 - 386
6534F374 - 386
1141A424 - 432
2141B424 - 432
3141C424 - 432
4141D424 - 432
5141E424 - 432
6141F424 - 432
1241A444 - 574
2241B444 - 574
3241C444 - 574
4241D444 - 574
5241E444 - 574
6241F444 - 574
1341A585 - 619
2341B585 - 619
3341C585 - 619
4341D585 - 619
5341E585 - 619
6341F585 - 619
1444A626 - 691
2444B626 - 691
3444C626 - 691
4444D626 - 691
5444E626 - 691
6444F626 - 691
1154A433 - 443
2154B433 - 443
3154C433 - 443
4154D433 - 443
5154E433 - 443
6154F433 - 443
1254A575 - 584
2254B575 - 584
3254C575 - 584
4254D575 - 584
5254E575 - 584
6254F575 - 584
1354A620 - 625
2354B620 - 625
3354C620 - 625
4354D620 - 625
5354E620 - 625
6354F620 - 625

NCS ensembles :
ID
1
2
3
4
5

NCS oper:
IDCodeMatrixVector
1given(-0.9858, -0.04493, -0.16179), (-0.04436, 0.99899, -0.00714), (0.16195, 0.00013, -0.9868)-61.88751, 55.96052, -99.51503
2given(0.33799, 0.01381, 0.94105), (-0.09495, 0.99529, 0.01949), (-0.93635, -0.09594, 0.33771)57.70181, 12.23866, -118.23937
3given(-0.4735, 0.00167, -0.88079), (-0.05678, 0.99786, 0.03242), (0.87896, 0.06536, -0.47239)-118.28419, 80.18089, 0.21715
4given(-0.46401, -0.00026, 0.88583), (-0.02436, 0.99963, -0.01247), (-0.88549, -0.02736, -0.46385)-56.26374, 40.01058, -105.86585
5given(0.59319, 0.01957, -0.80482), (-0.04287, 0.99905, -0.0073), (0.80392, 0.03883, 0.59347)11.48757, 97.01311, -3.3822

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Components

#1: Protein
RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE EPSILON / PROTEIN-TYROSINE PHOSPHATASE EPSILON / R-PTP -EPSILON / PROTEIN TYROSINE PHOSPHATASE / RECEPTOR ...PROTEIN-TYROSINE PHOSPHATASE EPSILON / R-PTP -EPSILON / PROTEIN TYROSINE PHOSPHATASE / RECEPTOR TYPE / E ISOFORM


Mass: 69600.383 Da / Num. of mol.: 6 / Fragment: RESIDUES 107-697
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-CH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: P23469, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
Has protein modificationY
Sequence detailsTHERE IS A MUTATION OF GLU->GLY AT RESIDUE 581 (CLONING ERROR)

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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: 5.13 Å3/Da / Density % sol: 75.84 % / Description: NONE
Crystal growpH: 6.5 / Details: 1.60 M MGSO4, 0.1 M MES PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9537
DetectorType: MARRESEARCH / 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: 3.2→34.65 Å / Num. obs: 373908 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 9
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.5 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→218.22 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.884 / SU B: 41.207 / SU ML: 0.315 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.158 / ESU R Free: 0.4 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 5502 5 %RANDOM
Rwork0.221 ---
obs0.223 104282 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.37 Å2
Baniso -1Baniso -2Baniso -3
1--3.9 Å20 Å22.51 Å2
2--5.05 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 3.2→218.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23738 0 12 0 23750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02124353
X-RAY DIFFRACTIONr_bond_other_d0.0010.0215151
X-RAY DIFFRACTIONr_angle_refined_deg1.1691.92533330
X-RAY DIFFRACTIONr_angle_other_deg0.871336749
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44853199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.2122.587924
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.566153134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.41215122
X-RAY DIFFRACTIONr_chiral_restr0.0630.23850
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02127893
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025329
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2021.516133
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.396225372
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.63538220
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.0444.57958
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A263tight positional0.020.05
12B263tight positional0.020.05
13C263tight positional0.020.05
14D263tight positional0.020.05
15E263tight positional0.020.05
16F263tight positional0.030.05
21A2530tight positional0.020.05
22B2530tight positional0.020.05
23C2530tight positional0.020.05
24D2530tight positional0.020.05
25E2530tight positional0.020.05
26F2530tight positional0.020.05
41A1959tight positional0.220.05
42B1959tight positional0.210.05
43C1959tight positional0.210.05
44D1959tight positional0.20.05
45E1959tight positional0.230.05
46F1959tight positional0.220.05
31A480medium positional0.330.5
32B480medium positional0.460.5
33C480medium positional0.390.5
34D480medium positional0.290.5
35E480medium positional0.290.5
36F480medium positional0.280.5
41A813medium positional0.20.5
42B813medium positional0.20.5
43C813medium positional0.210.5
44D813medium positional0.190.5
45E813medium positional0.180.5
46F813medium positional0.20.5
51A201medium positional0.450.5
52B201medium positional0.310.5
53C201medium positional0.470.5
54D201medium positional0.290.5
55E201medium positional0.280.5
56F201medium positional0.430.5
11A263tight thermal0.030.5
12B263tight thermal0.030.5
13C263tight thermal0.030.5
14D263tight thermal0.030.5
15E263tight thermal0.020.5
16F263tight thermal0.030.5
21A2530tight thermal0.030.5
22B2530tight thermal0.030.5
23C2530tight thermal0.030.5
24D2530tight thermal0.030.5
25E2530tight thermal0.030.5
26F2530tight thermal0.030.5
41A1959tight thermal0.210.5
42B1959tight thermal0.180.5
43C1959tight thermal0.190.5
44D1959tight thermal0.190.5
45E1959tight thermal0.190.5
46F1959tight thermal0.170.5
31A480medium thermal0.22
32B480medium thermal0.192
33C480medium thermal0.22
34D480medium thermal0.172
35E480medium thermal0.192
36F480medium thermal0.162
41A813medium thermal0.192
42B813medium thermal0.182
43C813medium thermal0.212
44D813medium thermal0.182
45E813medium thermal0.192
46F813medium thermal0.182
51A201medium thermal0.192
52B201medium thermal0.192
53C201medium thermal0.182
54D201medium thermal0.152
55E201medium thermal0.142
56F201medium thermal0.172
LS refinement shellResolution: 3.2→3.28 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.361 345
Rwork0.341 6911
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)
13.42741.03420.60413.07591.27065.95580.09790.0805-0.14-0.1290.09690.0642-0.1058-0.1098-0.1947-0.29430.0275-0.161-0.1424-0.0531-0.2083-70.346-37.431-47.336
23.5588-0.0495-0.4474.4475-0.0652.22470.12260.24680.0343-0.2388-0.07-0.0932-0.1175-0.1285-0.0526-0.20450.0111-0.0692-0.10250.0224-0.3329-45.061-9.379-52.817
32.9247-0.59110.16491.923-0.02455.03140.1158-0.0383-0.1331-0.0299-0.0301-0.11240.10810.2497-0.0858-0.2804-0.0344-0.1529-0.11930.0295-0.195916.84121.973-63.574
42.7916-0.4554-0.3165.3675-0.00712.5940.0809-0.5188-0.05940.3483-0.01060.1883-0.364-0.0386-0.0703-0.19350.001-0.05830.104-0.0975-0.3125-8.40648.749-54.652
56.22761.0270.41331.8048-0.13293.9585-0.2099-0.3416-0.3940.0394-0.0409-0.0285-0.0314-0.19760.2508-0.13330.0418-0.0112-0.1927-0.015-0.2217-11.643-19.226-64.864
62.7921-0.02810.08284.99080.44863.4117-0.08440.21960.1669-0.2256-0.12850.3012-0.0748-0.42270.2129-0.1740.0282-0.1645-0.01970.0414-0.3554-7.3545.886-92.97
76.2634-1.2985-0.32992.79450.38744.1099-0.30560.3536-0.52470.08350.0371-0.01020.09320.15350.2685-0.2281-0.00410.0044-0.01050.0198-0.1222-43.77445.631-42.281
82.4947-0.3852-0.12874.91170.08284.07550.0223-0.34240.13210.3348-0.2145-0.24790.00910.43960.1923-0.1636-0.0626-0.14450.0987-0.065-0.3134-50.62771.495-14.995
93.5930.0308-0.72082.3378-0.79833.8645-0.0727-0.27370.08410.13550.12320.07740.17790.1478-0.0505-0.11290.0401-0.1244-0.0598-0.0517-0.33-65.0235.193-20.658
103.61580.07070.63744.27410.04342.5410.0854-0.42530.53460.0337-0.00120.2315-0.0149-0.0924-0.0841-0.26110.0457-0.0779-0.0842-0.0907-0.1947-81.96732.307-41.433
113.49320.1591-0.62852.82730.9474.1885-0.04010.20090.1129-0.22140.0978-0.08820.0989-0.0554-0.0576-0.06620.0184-0.1635-0.1632-0.004-0.35716.79263.321-89.564
123.5196-0.1340.16415.3808-0.18813.20710.23060.44380.3789-0.3006-0.0332-0.4179-0.06370.3186-0.1974-0.255-0.0563-0.08480.10330.0132-0.194826.92489.699-71.046
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A112 - 406
2X-RAY DIFFRACTION2A425 - 691
3X-RAY DIFFRACTION3B111 - 406
4X-RAY DIFFRACTION4B425 - 691
5X-RAY DIFFRACTION5C111 - 406
6X-RAY DIFFRACTION6C425 - 691
7X-RAY DIFFRACTION7D112 - 406
8X-RAY DIFFRACTION8D425 - 691
9X-RAY DIFFRACTION9E111 - 406
10X-RAY DIFFRACTION10E425 - 691
11X-RAY DIFFRACTION11F111 - 406
12X-RAY DIFFRACTION12F425 - 691

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