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- PDB-2yd5: Crystal structure of the N-terminal Ig1-2 module of Human Recepto... -

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Basic information

Entry
Database: PDB / ID: 2yd5
TitleCrystal structure of the N-terminal Ig1-2 module of Human Receptor Protein Tyrosine Phosphatase LAR
ComponentsRECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE F
KeywordsHYDROLASE
Function / homology
Function and homology information


chondroitin sulfate proteoglycan binding / cell surface receptor protein tyrosine phosphatase signaling pathway / neuron projection regeneration / Receptor-type tyrosine-protein phosphatases / transmembrane receptor protein tyrosine phosphatase activity / synaptic membrane adhesion / Synaptic adhesion-like molecules / regulation of axon regeneration / peptidyl-tyrosine dephosphorylation / phosphoprotein phosphatase activity ...chondroitin sulfate proteoglycan binding / cell surface receptor protein tyrosine phosphatase signaling pathway / neuron projection regeneration / Receptor-type tyrosine-protein phosphatases / transmembrane receptor protein tyrosine phosphatase activity / synaptic membrane adhesion / Synaptic adhesion-like molecules / regulation of axon regeneration / peptidyl-tyrosine dephosphorylation / phosphoprotein phosphatase activity / cell adhesion molecule binding / Insulin receptor recycling / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / negative regulation of receptor binding / cell migration / heparin binding / cell adhesion / neuron projection / neuronal cell body / protein-containing complex binding / signal transduction / extracellular exosome / plasma membrane
Similarity search - Function
: / 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, 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
Receptor-type tyrosine-protein phosphatase F
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Oct 23, 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

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Assembly

Deposited unit
A: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE F


Theoretical massNumber of molelcules
Total (without water)23,3801
Polymers23,3801
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.950, 76.950, 68.740
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE F / RECEPTOR PROTEIN TYROSINE PHOSPHATASE LAR / LEUKOCYTE COMMON ANTIGEN RELATED / LAR / RPTP LAR


Mass: 23380.301 Da / Num. of mol.: 1 / Fragment: IG1-2, RESIDUES 29-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: P10586, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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) DERIVE 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: 2.51 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 5.6
Details: 0.1 M SODIUM ACETATE TRIHYDRATE, 20% ISOPROPANOL, 20% (W/V) PEG 4000, 0.25 MM HEPARIN DP10, PH 5.6 .

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9765
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.2→48 Å / Num. obs: 12272 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Biso Wilson estimate: 33.23 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.1
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 3.6 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
XDSdata reduction
xia2data scaling
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YD4

2yd4


Resolution: 2.2→38.475 Å / SU ML: 0.26 / σ(F): 0 / Phase error: 21.72 / Stereochemistry target values: ML
Details: THE SIDECHAIN OF ARG228 IS DISORDERED AND IS NOT INCLUDED IN THE CRYSTAL STRUCTURE.
RfactorNum. reflection% reflection
Rfree0.2326 566 4.8 %
Rwork0.1955 --
obs0.1973 11699 95.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso mean: 39.13 Å2
Baniso -1Baniso -2Baniso -3
1-5.9418 Å20 Å20 Å2
2--5.9418 Å20 Å2
3----10.1376 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1510 0 0 59 1569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041549
X-RAY DIFFRACTIONf_angle_d0.8272097
X-RAY DIFFRACTIONf_dihedral_angle_d12.871589
X-RAY DIFFRACTIONf_chiral_restr0.054232
X-RAY DIFFRACTIONf_plane_restr0.003281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2004-2.42180.30861240.23352531X-RAY DIFFRACTION88
2.4218-2.77220.27821390.23172723X-RAY DIFFRACTION94
2.7722-3.49230.24251640.20512854X-RAY DIFFRACTION98
3.4923-38.48090.19791390.17353025X-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)
11.61130.5905-0.13380.72460.17460.86350.11420.2040.01540.0844-0.04850.05820.1114-0.0034-0.06940.20420.0319-0.00820.18930.00440.159228.9136-20.7002-14.7476
21.23960.2169-0.36040.4771-0.2991.34970.12140.00180.2542-0.0838-0.1389-0.0262-0.4752-0.04060.00290.33730.04460.0330.18520.01020.19231.7351-1.4777-5.3862
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 30:126)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 127:228)

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