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- PDB-2ooq: Crystal Structure of the Human Receptor Phosphatase PTPRT -

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Basic information

Entry
Database: PDB / ID: 2ooq
TitleCrystal Structure of the Human Receptor Phosphatase PTPRT
ComponentsReceptor-type tyrosine-protein phosphatase T
KeywordsHYDROLASE / Protein Tyrosine Phosphatase / receptor / Human / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


thiolester hydrolase activity / gamma-catenin binding / transmembrane receptor protein tyrosine phosphatase activity / delta-catenin binding / alpha-catenin binding / cellular response to interleukin-6 / negative regulation of receptor signaling pathway via STAT / STAT family protein binding / homophilic cell-cell adhesion / alpha-actinin binding ...thiolester hydrolase activity / gamma-catenin binding / transmembrane receptor protein tyrosine phosphatase activity / delta-catenin binding / alpha-catenin binding / cellular response to interleukin-6 / negative regulation of receptor signaling pathway via STAT / STAT family protein binding / homophilic cell-cell adhesion / alpha-actinin binding / peptidyl-tyrosine dephosphorylation / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cell surface receptor protein tyrosine kinase signaling pathway / negative regulation of cell migration / beta-catenin binding / neuron projection development / protein phosphatase binding / cell adhesion / cadherin binding / cell surface / signal transduction / protein homodimerization activity / membrane / plasma membrane
Similarity search - Function
: / Receptor-type tyrosine-protein phosphatase U Fn3 domain / MAM domain signature. / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain ...: / Receptor-type tyrosine-protein phosphatase U Fn3 domain / MAM domain signature. / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / 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 profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase T
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsUgochukwu, E. / Alfano, I. / Barr, A. / Keates, T. / Eswaran, J. / Salah, E. / Savitsky, P. / Bunkoczi, G. / Edwards, A. / Arrowsmith, C.H. ...Ugochukwu, E. / Alfano, I. / Barr, A. / Keates, T. / Eswaran, J. / Salah, E. / Savitsky, P. / Bunkoczi, G. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / von Delft, F. / Knapp, S. / Structural Genomics Consortium (SGC)
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. / Filippakopoulos, P. / Alfano, I. / Savitsky, P. / Burgess-Brown, N.A. / Muller, S. / Knapp, S.
History
DepositionJan 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Aug 30, 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_ncs_dom_lim / struct_ref_seq_dif / 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_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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _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 T
B: Receptor-type tyrosine-protein phosphatase T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1766
Polymers65,5262
Non-polymers6504
Water7,855436
1
A: Receptor-type tyrosine-protein phosphatase T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0452
Polymers32,7631
Non-polymers2821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Receptor-type tyrosine-protein phosphatase T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1304
Polymers32,7631
Non-polymers3673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.186, 86.697, 91.120
Angle α, β, γ (deg.)90.00, 99.89, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETARGARGAA889 - 9052 - 18
21METMETARGARGBB889 - 9052 - 18
32PHEPHESERSERAA911 - 107124 - 184
42PHEPHESERSERBB911 - 107124 - 184
53PROPROCYSCYSAA1078 - 1168191 - 281
63PROPROCYSCYSBB1078 - 1168191 - 281

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Components

#1: Protein Receptor-type tyrosine-protein phosphatase T / R-PTP-T / RPTP-rho


Mass: 32763.082 Da / Num. of mol.: 2 / Fragment: PTPRT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRT, KIAA0283 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta (DE3) / References: UniProt: O14522, protein-tyrosine-phosphatase
#2: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.21 Å3/Da / Density % sol: 44.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M LiCl, 0.1M HEPES, 20.0% PEG 6000, 10.0% Ethylene glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→89.77 Å / Num. obs: 52802 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 16
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.595 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalClear(MSC/RIGAKU)data collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1RPM, 2C7S, 1LAR, 2FH7

1rpm

2c7s

1lar

2fh7


Resolution: 1.8→89.77 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.669 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18758 2688 5.1 %RANDOM
Rwork0.14488 ---
all0.14709 50081 --
obs0.14709 50081 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.417 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å2-0.35 Å2
2--0.3 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.8→89.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4421 0 35 436 4892
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224602
X-RAY DIFFRACTIONr_bond_other_d0.0020.023082
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.9416257
X-RAY DIFFRACTIONr_angle_other_deg0.9093.0027431
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.45562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.44623.612227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17815742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2861535
X-RAY DIFFRACTIONr_chiral_restr0.0890.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025141
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02968
X-RAY DIFFRACTIONr_nbd_refined0.2170.2899
X-RAY DIFFRACTIONr_nbd_other0.2020.23230
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22262
X-RAY DIFFRACTIONr_nbtor_other0.0850.22349
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2339
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0930.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.260.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.211
X-RAY DIFFRACTIONr_mcbond_it3.65152791
X-RAY DIFFRACTIONr_mcbond_other1.83951134
X-RAY DIFFRACTIONr_mcangle_it4.81674524
X-RAY DIFFRACTIONr_scbond_it7.12291884
X-RAY DIFFRACTIONr_scangle_it8.471111730
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1571medium positional0.170.5
1858loose positional0.385
1571medium thermal1.432
1858loose thermal2.6510
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 196 -
Rwork0.193 3729 -
obs--99.75 %
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)
10.60750.14520.03340.70070.33682.85820.10050.00580.17670.0939-0.02320.0528-0.3328-0.1288-0.0774-0.00160.00260.0362-0.01640.00370.008314.10454.296590.3753
20.58430.129-0.01510.5080.02530.9607-0.01790.0222-0.0211-0.03130.01260.01650.01460.02840.0053-0.10910.0078-0.011-0.10210.0013-0.0694-4.5917-9.809944.8135
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA889 - 11682 - 281
2X-RAY DIFFRACTION2BB888 - 11681 - 281

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