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- PDB-3i7z: Protein Tyrosine Phosphatase 1B - Transition state analog for the... -

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Basic information

Entry
Database: PDB / ID: 3i7z
TitleProtein Tyrosine Phosphatase 1B - Transition state analog for the first catalytic step
Components
  • EGFR receptor fragment
  • Tyrosine-protein phosphatase non-receptor type 1
KeywordsHYDROLASE / P-loop / WPD-loop / Protein Phosphatase / EGFR receptor / Vanadate / Acetylation / Endoplasmic reticulum / Membrane / Oxidation / Phosphoprotein / Polymorphism
Function / homology
Function and homology information


regulation of hepatocyte growth factor receptor signaling pathway / PTK6 Down-Regulation / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of PERK-mediated unfolded protein response / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / cytoplasmic side of endoplasmic reticulum membrane ...regulation of hepatocyte growth factor receptor signaling pathway / PTK6 Down-Regulation / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of PERK-mediated unfolded protein response / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / cytoplasmic side of endoplasmic reticulum membrane / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / mitochondrial crista / positive regulation of IRE1-mediated unfolded protein response / regulation of type I interferon-mediated signaling pathway / regulation of endocytosis / non-membrane spanning protein tyrosine phosphatase activity / positive regulation of protein tyrosine kinase activity / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling / regulation of signal transduction / cellular response to unfolded protein / growth hormone receptor signaling pathway via JAK-STAT / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of signal transduction / Regulation of IFNG signaling / Growth hormone receptor signaling / MECP2 regulates neuronal receptors and channels / endoplasmic reticulum unfolded protein response / positive regulation of JUN kinase activity / Insulin receptor recycling / negative regulation of insulin receptor signaling pathway / ephrin receptor binding / Integrin signaling / protein dephosphorylation / protein-tyrosine-phosphatase / negative regulation of MAP kinase activity / protein phosphatase 2A binding / protein tyrosine phosphatase activity / endosome lumen / insulin receptor binding / Negative regulation of MET activity / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / insulin receptor signaling pathway / actin cytoskeleton organization / early endosome / mitochondrial matrix / cadherin binding / protein kinase binding / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-1/2 / 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, non-receptor type-1/2 / 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
VANADATE ION / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsBrandao, T.A.S. / Johnson, S.J. / Hengge, A.C.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Insights into the reaction of protein-tyrosine phosphatase 1B: crystal structures for transition state analogs of both catalytic steps.
Authors: Brandao, T.A. / Hengge, A.C. / Johnson, S.J.
History
DepositionJul 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn.ptnr2_label_seq_id / _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: Tyrosine-protein phosphatase non-receptor type 1
B: EGFR receptor fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6347
Polymers38,0902
Non-polymers5435
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Tyrosine-protein phosphatase non-receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7875
Polymers37,3661
Non-polymers4214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: EGFR receptor fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8472
Polymers7251
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.020, 88.020, 118.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Tyrosine-protein phosphatase non-receptor type 1 / Protein-tyrosine phosphatase 1B / PTP-1B


Mass: 37365.637 Da / Num. of mol.: 1 / Fragment: Residues 1-321
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTP1B, PTPN1 / Plasmid: pET-19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P18031, protein-tyrosine-phosphatase
#2: Protein/peptide EGFR receptor fragment


Mass: 724.714 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 155 molecules

#3: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 3.45 Å3/Da / Density % sol: 64.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Drop: 2 uL of protein solution, 0.5 uL sucrose 30% (w/v) and 3 uL of precipitant solution (0.1 M HEPES pH 7.5, 0.2 M magnesium acetate and 15-17% polyethylene glycol 8000). Well: 500 uL of ...Details: Drop: 2 uL of protein solution, 0.5 uL sucrose 30% (w/v) and 3 uL of precipitant solution (0.1 M HEPES pH 7.5, 0.2 M magnesium acetate and 15-17% polyethylene glycol 8000). Well: 500 uL of precipitant solution. The protein solution was prepared as follows: 0.36 uL of 100 mM of Na3VO4 and 10 uL of 50 mM of DADEYL peptide (at pH 8.5-9.0) were mixed and allowed to react for 1-1.5 hour; then, 50 uL of native PTP1B (12 mg/mL in 10 mM Tris pH 7.5, 25 mM NaCl, 0.2 mM EDTA and 3 mM DTT) was added and the solution used immediately for crystallization. VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 13, 2008 / Details: mirrors
RadiationMonochromator: OSMIC BLUE OPTICS / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 5.58 % / Number: 136054 / Rmerge(I) obs: 0.075 / Χ2: 1 / D res high: 2.3 Å / D res low: 29.43 Å / Num. obs: 24185 / % possible obs: 99.9
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)% possible obs (%)Rmerge(I) obsChi squaredRedundancyRejects
4.9529.4399.60.0370.715.46149
3.934.9599.90.0490.75.6660
3.433.9399.90.0740.745.6651
3.123.431000.1130.885.5495
2.93.121000.1710.985.6389
2.732.91000.2841.15.6274
2.592.731000.3561.155.5868
2.482.591000.4411.265.51242
2.382.481000.4681.25.5885
2.32.381000.541.295.58109
ReflectionResolution: 2.3→29.43 Å / Num. all: 24185 / Num. obs: 24185 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.58 % / Biso Wilson estimate: 59.3 Å2 / Rmerge(I) obs: 0.075 / Χ2: 1 / Net I/σ(I): 9.2 / Scaling rejects: 1022
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.58 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.3 / Num. measured all: 13534 / Num. unique all: 2405 / Χ2: 1.29 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å27.64 Å
Translation2.5 Å27.64 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata scaling
PHASER1.3.3phasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CM2

2cm2


Resolution: 2.3→27.637 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.783 / SU ML: 0.4 / σ(F): 1.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1234 5.11 %RANDOM
Rwork0.206 ---
all0.207 24156 --
obs0.207 24156 52.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.3 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso max: 207.84 Å2 / Biso mean: 75.083 Å2 / Biso min: 37.87 Å2
Baniso -1Baniso -2Baniso -3
1--6.908 Å20 Å20 Å2
2---6.908 Å2-0 Å2
3---8.994 Å2
Refinement stepCycle: LAST / Resolution: 2.3→27.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2477 0 32 150 2659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092561
X-RAY DIFFRACTIONf_angle_d1.2683450
X-RAY DIFFRACTIONf_chiral_restr0.079362
X-RAY DIFFRACTIONf_plane_restr0.005443
X-RAY DIFFRACTIONf_dihedral_angle_d18.064965
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.3910.3491250.3362544266952
2.391-2.50.3141360.2962497263352
2.5-2.6320.3051290.2962497262652
2.632-2.7960.3081460.2682513265952
2.796-3.0120.3061330.2582524265752
3.012-3.3150.281570.2382528268553
3.315-3.7930.2441430.1912549269253
3.793-4.7750.1611450.1522571271654
4.775-27.6390.1851200.1562699281955
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)
10.1678-0.01230.0540.13250.05850.05670.39910.03420.31130.1841-0.0569-0.13540.0063-0.2302-00.48070.14520.1740.66930.08270.6831-15.1746-9.8832-8.8728
20.06840.1088-0.13220.1219-0.0039-0.0154-0.01950.2818-0.02880.7476-0.1801-0.15790.0109-0.876500.42680.01890.01220.8644-0.00190.4867-22.2273-27.8128-8.6173
30.05740.0129-0.0347-0.0017-0.05980.05-0.52110.6444-0.6640.1268-0.2328-0.429-0.1078-0.035800.3083-0.14850.15620.76220.07790.8938-15.8004-48.4971-9.7383
40.09590.1492-0.20390.31520.20560.0478-0.2427-0.3317-0.7270.09460.29540.4669-0.0793-0.6764-00.31670.01340.03150.99660.05370.5785-11.6127-41.9136-8.8352
5-0.03030.11520.05-0.09130.08080.1027-0.42680.2382-0.65570.07650.63310.3569-0.0104-0.5036-00.2823-0.05580.05670.9246-0.19450.7484-9.8821-49.8823-20.2578
61.1786-0.2349-0.95070.3316-0.01190.299-0.19110.1205-0.11770.05340.1174-0.02370.0530.0536-00.2410.0042-0.02710.8362-0.08060.4168-1.5971-37.3853-16.2913
70.2636-0.22660.19590.0027-0.1450.3839-0.479-0.39910.0863-0.159-0.04840.4250.27020.5241-00.30170.09650.08840.9867-0.08160.629712.2287-45.2278-19.0383
80.9682-1.014-1.08020.7577-0.17210.25680.02890.30570.1935-0.0060.098-0.18630.00050.1896-00.2495-0.0495-0.00610.8856-0.04940.44252.8326-29.4556-19.2286
9-0.05790.0463-0.00330.0342-0.0620.08060.2633-0.02730.0861-0.1212-0.2643-0.0586-0.0761-0.4594-00.44420.14420.00420.90030.15440.5254-14.2705-15.2306-24.4698
10-0.044-0.52030.17790.95710.9102-0.0741-0.21890.30430.0582-0.07360.082-0.4375-0.0351-0.0012-00.2993-0.0458-0.00180.76550.08010.5857-4.3971-17.5021-16.5877
110.00460.09510.0053-0.0676-0.1039-0.0526-0.2270.3098-0.99980.3591-0.07060.5467-0.17630.06930.00010.69530.02610.080.77920.19750.8884-8.29-36.67070.1512
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:20)A2 - 20
2X-RAY DIFFRACTION2(chain A and resid 21:31)A21 - 31
3X-RAY DIFFRACTION3(chain A and resid 32:40)A32 - 40
4X-RAY DIFFRACTION4(chain A and resid 41:55)A41 - 55
5X-RAY DIFFRACTION5(chain A and resid 56:65)A56 - 65
6X-RAY DIFFRACTION6(chain A and resid 66:127)A66 - 127
7X-RAY DIFFRACTION7(chain A and resid 128:147)A128 - 147
8X-RAY DIFFRACTION8(chain A and resid 148:230)A148 - 230
9X-RAY DIFFRACTION9(chain A and resid 231:248)A231 - 248
10X-RAY DIFFRACTION10(chain A and resid 249:298)A249 - 298
11X-RAY DIFFRACTION11(chain B)B0

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