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- PDB-2yd1: Crystal structure of the N-terminal Ig1-2 module of Drosophila Re... -

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Basic information

Entry
Database: PDB / ID: 2yd1
TitleCrystal structure of the N-terminal Ig1-2 module of Drosophila Receptor Protein Tyrosine Phosphatase DLAR
ComponentsTYROSINE-PROTEIN PHOSPHATASE LAR
KeywordsHYDROLASE
Function / homology
Function and homology information


centripetally migrating follicle cell migration / negative regulation of homophilic cell adhesion / Receptor-type tyrosine-protein phosphatases / positive regulation of plasma membrane bounded cell projection assembly / R7 cell development / Other semaphorin interactions / Synaptic adhesion-like molecules / NCAM signaling for neurite out-growth / Insulin receptor recycling / RAF/MAP kinase cascade ...centripetally migrating follicle cell migration / negative regulation of homophilic cell adhesion / Receptor-type tyrosine-protein phosphatases / positive regulation of plasma membrane bounded cell projection assembly / R7 cell development / Other semaphorin interactions / Synaptic adhesion-like molecules / NCAM signaling for neurite out-growth / Insulin receptor recycling / RAF/MAP kinase cascade / photoreceptor cell morphogenesis / regulation of axon extension involved in axon guidance / SAM domain binding / axon target recognition / synaptic assembly at neuromuscular junction / Neutrophil degranulation / transmembrane receptor protein tyrosine phosphatase activity / hematopoietic stem cell homeostasis / motor neuron axon guidance / retinal ganglion cell axon guidance / axon extension / positive regulation of filopodium assembly / oogenesis / cell leading edge / protein-tyrosine-phosphatase / negative regulation of insulin receptor signaling pathway / protein tyrosine phosphatase activity / axon guidance / basal plasma membrane / insulin receptor binding / nervous system development / heparin binding / spermatogenesis / cell adhesion / axon / focal adhesion / cell surface / signal transduction
Similarity search - Function
: / Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif ...: / Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Immunoglobulin I-set / Immunoglobulin I-set 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 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
GLYCINE / Tyrosine-protein phosphatase Lar
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsColes, C.H. / Shen, Y. / Tenney, A.P. / Siebold, C. / Sutton, G.C. / Lu, W. / Gallagher, J.T. / Jones, E.Y. / Flanagan, J.G. / Aricescu, A.R.
CitationJournal: Science / Year: 2011
Title: Proteoglycan-Specific Molecular Switch for Rptp Sigma Clustering and Neuronal Extension.
Authors: Coles, C.H. / Shen, Y. / Tenney, A.P. / Siebold, C. / Sutton, G.C. / Lu, W. / Gallagher, J.T. / Jones, E.Y. / Flanagan, J.G. / Aricescu, A.R.
History
DepositionMar 17, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TYROSINE-PROTEIN PHOSPHATASE LAR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3222
Polymers23,2471
Non-polymers751
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.201, 29.074, 49.408
Angle α, β, γ (deg.)90.00, 107.29, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TYROSINE-PROTEIN PHOSPHATASE LAR / RECEPTOR PROTEIN TYROSINE PHOSPHATASE DLAR / PROTEIN-TYROSINE-PHOSPHATE PHOSPHOHYDROLASE / DLAR / RPTP


Mass: 23247.146 Da / Num. of mol.: 1 / Fragment: IG1-2, RESIDUES 33-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: P16621, protein-tyrosine-phosphatase
#2: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE N-TERMINAL THREE AMINO ACID RESIDUES (ETG) AND THE C- TERMINAL NINE AMINO ACID RESIDUES ...THE N-TERMINAL THREE AMINO ACID RESIDUES (ETG) AND THE C- TERMINAL NINE AMINO ACID RESIDUES (GTKHHHHHH) ARE DERIVED FROM THE PHLSEC VECTOR

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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: 1.83 Å3/Da / Density % sol: 34 % / Description: NONE
Crystal growpH: 5
Details: 25% W/V PEG 1500, 0.1M SPG SYSTEM, 35MM AMMONIUM SULPHATE, PH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 16271 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 20.29 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.6
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YD4

2yd4


Resolution: 1.8→47.175 Å / SU ML: 0.21 / σ(F): 0 / Phase error: 25.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2233 720 4.7 %
Rwork0.1798 --
obs0.1819 15362 95.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso mean: 31.96 Å2
Baniso -1Baniso -2Baniso -3
1--8.6194 Å20 Å2-1.8064 Å2
2--15.7053 Å20 Å2
3----8.652 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1498 0 5 116 1619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061545
X-RAY DIFFRACTIONf_angle_d1.1232098
X-RAY DIFFRACTIONf_dihedral_angle_d12.143586
X-RAY DIFFRACTIONf_chiral_restr0.079230
X-RAY DIFFRACTIONf_plane_restr0.005280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.9390.28121350.22052695X-RAY DIFFRACTION89
1.939-2.13410.27241340.17552846X-RAY DIFFRACTION94
2.1341-2.4430.23821350.18512959X-RAY DIFFRACTION97
2.443-3.07780.24191370.19143019X-RAY DIFFRACTION99
3.0778-47.19110.1961790.16723123X-RAY DIFFRACTION100
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)
10.27420.19690.00130.13480.03050.4815-0.04430.1892-0.0921-0.0234-0.07270.0151-0.0265-0.1236-0.05880.190.03480.00910.1657-0.02610.158550.19866.44335.8559
20.3056-0.1741-0.00790.3082-0.20620.17070.0629-0.1587-0.0819-0.0353-0.01380.08280.0201-0.20470.00320.1290.0264-0.00910.1786-0.00470.158431.819613.254517.9859
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 34:129)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 130:229)

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