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- PDB-3pxj: Tandem Ig repeats of Dlar -

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Basic information

Entry
Database: PDB / ID: 3pxj
TitleTandem Ig repeats of Dlar
ComponentsTyrosine-protein phosphatase Lar
KeywordsHYDROLASE / Ig domains / Cell adhesion / Receptor protein tyrosine phosphatase
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 / Insulin receptor recycling / NCAM signaling for neurite out-growth / Other semaphorin interactions / R7 cell development / Synaptic adhesion-like molecules / 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 / Insulin receptor recycling / NCAM signaling for neurite out-growth / Other semaphorin interactions / R7 cell development / Synaptic adhesion-like molecules / RAF/MAP kinase cascade / photoreceptor cell morphogenesis / regulation of axon extension involved in axon guidance / SAM domain binding / axon target recognition / hematopoietic stem cell homeostasis / Neutrophil degranulation / transmembrane receptor protein tyrosine phosphatase activity / synaptic assembly at neuromuscular junction / axon extension / motor neuron axon guidance / positive regulation of filopodium assembly / retinal ganglion cell axon guidance / oogenesis / cell leading edge / peptidyl-tyrosine dephosphorylation / negative regulation of insulin receptor signaling pathway / protein-tyrosine-phosphatase / basal plasma membrane / protein tyrosine phosphatase activity / axon guidance / insulin receptor binding / nervous system development / heparin binding / spermatogenesis / receptor complex / cell adhesion / axon / focal adhesion / cell surface
Similarity search - Function
Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Immunoglobulin I-set / Immunoglobulin I-set domain / 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. ...Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Immunoglobulin I-set / Immunoglobulin I-set domain / 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 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase Lar
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3003 Å
AuthorsBiersmith, B.H. / Bouyain, S.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The Immunoglobulin-like Domains 1 and 2 of the Protein Tyrosine Phosphatase LAR Adopt an Unusual Horseshoe-like Conformation.
Authors: Biersmith, B.H. / Hammel, M. / Geisbrecht, E.R. / Bouyain, S.
History
DepositionDec 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase Lar
B: Tyrosine-protein phosphatase Lar
C: Tyrosine-protein phosphatase Lar
D: Tyrosine-protein phosphatase Lar


Theoretical massNumber of molelcules
Total (without water)90,9704
Polymers90,9704
Non-polymers00
Water2,486138
1
A: Tyrosine-protein phosphatase Lar


Theoretical massNumber of molelcules
Total (without water)22,7431
Polymers22,7431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosine-protein phosphatase Lar


Theoretical massNumber of molelcules
Total (without water)22,7431
Polymers22,7431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tyrosine-protein phosphatase Lar


Theoretical massNumber of molelcules
Total (without water)22,7431
Polymers22,7431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Tyrosine-protein phosphatase Lar


Theoretical massNumber of molelcules
Total (without water)22,7431
Polymers22,7431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.957, 77.513, 81.726
Angle α, β, γ (deg.)90.000, 101.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Tyrosine-protein phosphatase Lar / Protein-tyrosine-phosphate phosphohydrolase / dLAR


Mass: 22742.623 Da / Num. of mol.: 4 / Fragment: Ig domains 1 and 2 (UNP Residues 32-237)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Lar, CG10443 / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2(DE3) / References: UniProt: P16621, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50 mM imidazole pH 7.0, 10 mM ammonium sulfate, 20% (w/v) PEG 2000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97242 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 25, 2010
RadiationMonochromator: ROSENBAUM-ROCK MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 39287 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.117 / Χ2: 1.008 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.3820.41538441.09398.2
2.38-2.482.30.40539641.04499.3
2.48-2.592.50.33839471.03199.6
2.59-2.732.70.26439510.99799.4
2.73-2.92.80.20739411.01599.5
2.9-3.122.80.16239451.02299.4
3.12-3.442.90.12839210.97499.1
3.44-3.932.90.10839430.92298.9
3.93-4.952.90.09439130.98498.1
4.95-502.90.10839181.05395.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 52.37
Highest resolutionLowest resolution
Rotation2.5 Å41.38 Å
Translation2.5 Å41.38 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
SERGUIdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PXH

3pxh


Resolution: 2.3003→41.385 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7146 / SU ML: 0.36 / σ(F): 0 / Phase error: 33.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2613 1844 4.97 %RANDOM
Rwork0.2233 ---
obs0.2251 37084 92.99 %-
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.026 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso max: 205.76 Å2 / Biso mean: 58.2339 Å2 / Biso min: 12.55 Å2
Baniso -1Baniso -2Baniso -3
1--3.2922 Å2-0 Å2-0.6795 Å2
2---7.0839 Å20 Å2
3---10.3761 Å2
Refinement stepCycle: LAST / Resolution: 2.3003→41.385 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5965 0 0 138 6103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0326097
X-RAY DIFFRACTIONf_angle_d1.6578262
X-RAY DIFFRACTIONf_chiral_restr0.135905
X-RAY DIFFRACTIONf_plane_restr0.0141096
X-RAY DIFFRACTIONf_dihedral_angle_d21.0282306
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3003-2.38250.38811590.33833057321682
2.3825-2.47790.45081750.33883304347987
2.4779-2.59060.40061770.31583356353389
2.5906-2.72720.33171820.29363513369593
2.7272-2.8980.35241870.27313561374894
2.898-3.12170.29381870.25613646383396
3.1217-3.43570.24391940.23393686388098
3.4357-3.93260.25311960.2033730392698
3.9326-4.95330.18071960.15643721391798
4.9533-41.39160.22431910.20913666385794
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)
11.10130.34090.35980.1434-1.09450.37720.2672-0.20740.255-0.001-0.131-0.1132-0.0768-0.0084-0.0530.1177-0.0361-0.07810.4669-0.02870.234738.10084.7175.8134
20.9805-1.3713-0.19771.42640.71540.85690.18650.13970.23080.01710.1064-0.5143-0.0288-0.0114-0.24560.1213-0.0333-0.06060.4320.02060.291223.963922.85810.1726
31.1881-1.0354-0.17940.9658-0.60250.99090.0666-0.04470.05070.0104-0.0795-0.23330.0960.03750.02260.1055-0.0235-0.02730.083-0.00550.164730.13786.894445.9239
40.7461-0.9005-0.28161.01910.67880.50240.1270.15440.1198-0.12140.19790.1628-0.0197-0.1926-0.25930.08810.0342-0.0243-0.0944-0.0540.173816.012924.945440.1993
50.1363-0.2077-0.16190.26820.08380.64530.09770.01340.2894-0.1909-0.12160.439-0.1841-0.01340.03920.1683-0.007-0.14540.09370.00770.4886-9.163922.879145.6445
61.6248-0.2980.43990.2632-0.15480.46540.08710.04230.1486-0.0555-0.03090.24670.11720.0448-0.09130.12080.0082-0.12470.04050.04570.38274.68514.441340.4479
71.378-1.25311.02410.8522-0.40050.37780.1422-0.05120.0906-0.0336-0.02680.16630.05810.2331-0.05540.13680.0077-0.13750.4205-0.03940.286212.15952.9022-0.3233
8-0.0009-0.08690.16680.0968-0.1313-0.68010.03190.1026-0.00620.0203-0.02530.01160.0290.0235-0.00110.1602-0.02530.05890.30390.0170.102512.374413.428424.7663
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 33:134A33 - 134
2X-RAY DIFFRACTION2chain A and resid 135:230A135 - 230
3X-RAY DIFFRACTION3chain B and resid 32:134B32 - 134
4X-RAY DIFFRACTION4chain B and resid 135:230B135 - 230
5X-RAY DIFFRACTION5chain C and resid 33:131C33 - 131
6X-RAY DIFFRACTION6chain C and resid 138:230C138 - 230
7X-RAY DIFFRACTION7chain D and resid 134:231D134 - 231
8X-RAY DIFFRACTION8chain EA - D1 - 262

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