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- PDB-2v5y: Crystal structure of the receptor protein tyrosine phosphatase mu... -

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Basic information

Entry
Database: PDB / ID: 2v5y
TitleCrystal structure of the receptor protein tyrosine phosphatase mu ectodomain
ComponentsRECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE MU
KeywordsHYDROLASE / MEMBRANE / RECEPTOR / GLYCOPROTEIN / RECEPTOR PROTEIN TYROSINE PHOSPHATASE / CELL ADHESION / TRANSMEMBRANE / PROTEIN PHOSPHATASE / EXTRACELLULAR REGION / IMMUNOGLOBULIN DOMAIN
Function / homology
Function and homology information


retina layer formation / transmembrane receptor protein tyrosine phosphatase activity / negative regulation of endothelial cell migration / retinal ganglion cell axon guidance / homophilic cell adhesion via plasma membrane adhesion molecules / negative regulation of endothelial cell proliferation / phosphatase activity / protein dephosphorylation / negative regulation of angiogenesis / protein-tyrosine-phosphatase ...retina layer formation / transmembrane receptor protein tyrosine phosphatase activity / negative regulation of endothelial cell migration / retinal ganglion cell axon guidance / homophilic cell adhesion via plasma membrane adhesion molecules / negative regulation of endothelial cell proliferation / phosphatase activity / protein dephosphorylation / negative regulation of angiogenesis / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / adherens junction / neuron projection development / cell-cell junction / lamellipodium / cadherin binding / response to xenobiotic stimulus / perinuclear region of cytoplasm / signal transduction / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Receptor-type tyrosine-protein phosphatase mu, PTPase domain, repeat 1 / : / MAM domain signature. / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Immunoglobulin / Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain ...Receptor-type tyrosine-protein phosphatase mu, PTPase domain, repeat 1 / : / MAM domain signature. / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Immunoglobulin / Immunoglobulin domain / 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 / Jelly Rolls - #200 / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase mu
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsAricescu, A.R. / Siebold, C. / Choudhuri, K. / Chang, V.T. / Lu, W. / Davis, S.J. / van der Merwe, P.A. / Jones, E.Y.
CitationJournal: Science / Year: 2007
Title: Structure of a Tyrosine Phosphatase Adhesive Interaction Reveals a Spacer-Clamp Mechanism.
Authors: Aricescu, A.R. / Siebold, C. / Choudhuri, K. / Chang, V.T. / Lu, W. / Davis, S.J. / Van Der Merwe, P.A. / Jones, E.Y.
History
DepositionJul 11, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE MU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,29410
Polymers81,6991
Non-polymers1,5949
Water00
1
A: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE MU
hetero molecules

A: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE MU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,58820
Polymers163,3992
Non-polymers3,18918
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area3710 Å2
ΔGint-10.9 kcal/mol
Surface area67200 Å2
MethodPQS
Unit cell
Length a, b, c (Å)167.336, 69.325, 97.487
Angle α, β, γ (deg.)90.00, 113.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE MU / PROTEIN-TYROSINE PHOSPHATASE MU / R-PTP-MU


Mass: 81699.344 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR REGION, RESIDUES 21-742
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: LUNG / Plasmid: PHLSEC / Cell line (production host): HEK-293S GNTI- / Production host: HOMO SAPIENS (human) / References: UniProt: P28827, protein-tyrosine-phosphatase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
Has protein modificationY

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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: 3.07 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 7
Details: 100MM BIS-TRIS-PROPANE, PH 6.5 22.5% (W/V) PEG-SMEAR, 200MM K-THIOCYANATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9794
DetectorType: ADSC CCD / Detector: CCD / Date: May 9, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. obs: 19030 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 10.3
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.5 / % possible all: 89

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
PHASERphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C9A

2c9a


Resolution: 3.1→20 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.81 / SU B: 48.964 / SU ML: 0.409 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.509 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32 969 5.2 %RANDOM
Rwork0.242 ---
obs0.246 17792 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.1 Å2
Baniso -1Baniso -2Baniso -3
1--5.03 Å20 Å2-1.94 Å2
2--5.12 Å20 Å2
3----1.63 Å2
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4423 0 100 0 4523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224649
X-RAY DIFFRACTIONr_bond_other_d0.0010.023137
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.9716350
X-RAY DIFFRACTIONr_angle_other_deg0.8363.0027590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6025562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45523.981211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.58415713
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1731529
X-RAY DIFFRACTIONr_chiral_restr0.0740.2703
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025208
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02926
X-RAY DIFFRACTIONr_nbd_refined0.1870.2947
X-RAY DIFFRACTIONr_nbd_other0.1870.23198
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22206
X-RAY DIFFRACTIONr_nbtor_other0.0870.22678
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.297
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2230.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.48122811
X-RAY DIFFRACTIONr_mcbond_other0.04121134
X-RAY DIFFRACTIONr_mcangle_it0.85834576
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.37821913
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.75231774
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
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 67 -
Rwork0.299 1294 -
obs--100 %
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)
11.5380.48440.11616.3608-2.12126.8369-0.0947-0.11640.31680.5441-0.3318-0.9645-0.43310.43510.42650.0498-0.095-0.14140.19820.11010.233222.02471.06912.417
22.21390.4261.17072.43850.30361.87780.0411-0.0340.06080.1594-0.0954-0.1960.02280.11820.05430.0866-0.00250.01950.21050.00460.1371209.84266.2957.827
35.0095-0.5496-0.42910.22390.24460.27530.0413-0.20690.05040.04230.0538-0.03930.1479-0.016-0.09510.1236-0.04240.09660.23220.04530.1355183.64563.5498.12
412.66240.3467-2.00531.00870.96731.3632-0.0692-0.2569-0.1633-0.19120.0529-0.13520.2070.10610.01630.0686-0.03390.08270.2047-0.0786-0.0114152.37369.67313.635
513.23024.5408-1.96482.4209-0.49491.37780.1667-0.6786-0.0326-0.0347-0.31290.18260.0244-0.07710.1461-0.0497-0.10540.09060.2663-0.13870.0447111.31659.4723.795
69.4969-0.5533-2.64581.84460.10553.89950.0536-0.22930.0213-0.11840.12660.0727-0.0840.2741-0.18010.1178-0.00250.05790.193-0.03060.027265.44249.8133.892
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 61
2X-RAY DIFFRACTION2A62 - 169
3X-RAY DIFFRACTION3A170 - 277
4X-RAY DIFFRACTION4A278 - 351
5X-RAY DIFFRACTION5A352 - 460
6X-RAY DIFFRACTION6A461 - 568

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