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- PDB-6x38: Crystal structure of the FN5 domain of Drosophila Lar -

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Basic information

Entry
Database: PDB / ID: 6x38
TitleCrystal structure of the FN5 domain of Drosophila Lar
ComponentsTyrosine-protein phosphatase Lar
KeywordsCELL ADHESION / Fibronectin type III / 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 / axon extension / synaptic assembly at neuromuscular junction / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Tyrosine-protein phosphatase Lar
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsBouyain, S. / Kawakami, J.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R21AR066264 United States
CitationJournal: Plos One / Year: 2022
Title: Complex protein interactions mediate Drosophila Lar function in muscle tissue.
Authors: Kawakami, J. / Brooks, D. / Zalmai, R. / Hartson, S.D. / Bouyain, S. / Geisbrecht, E.R.
History
DepositionMay 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase Lar
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1973
Polymers12,0661
Non-polymers1312
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.580, 42.658, 51.347
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 12066.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Lar, CG10443 / Production host: Escherichia coli (E. coli) / References: UniProt: P16621, protein-tyrosine-phosphatase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.84 Å3/Da / Density % sol: 33.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM HEPES pH 7.0, 200 mM Ammonium acetate, 3mM Zinc acetate, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 22169 / % possible obs: 98.4 % / Redundancy: 13 % / Biso Wilson estimate: 11.63 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 12.7
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 6.6 / Num. unique obs: 2127 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
PHENIX1.18.1_3865phasing
HKL-2000data reduction
HKL-2000data scaling
SERGUIdata collection
RefinementMethod to determine structure: SAD / Resolution: 1.3→32.81 Å / SU ML: 0.0895 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.4536
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1816 2004 9.07 %
Rwork0.1673 20096 -
obs0.1686 22100 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.91 Å2
Refinement stepCycle: LAST / Resolution: 1.3→32.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms711 0 2 110 823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014754
X-RAY DIFFRACTIONf_angle_d1.23231034
X-RAY DIFFRACTIONf_chiral_restr0.0957120
X-RAY DIFFRACTIONf_plane_restr0.0095135
X-RAY DIFFRACTIONf_dihedral_angle_d12.195282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.330.2281290.18591342X-RAY DIFFRACTION93.28
1.33-1.370.17171540.17351397X-RAY DIFFRACTION97.36
1.37-1.410.21311230.16441406X-RAY DIFFRACTION97.82
1.41-1.450.16421440.16471417X-RAY DIFFRACTION97.99
1.45-1.510.18071450.16291415X-RAY DIFFRACTION98.48
1.51-1.570.16691350.16461427X-RAY DIFFRACTION98.61
1.57-1.640.16441490.15971437X-RAY DIFFRACTION99.12
1.64-1.720.15671390.14871441X-RAY DIFFRACTION99.37
1.72-1.830.16971510.15611439X-RAY DIFFRACTION99.56
1.83-1.970.14631400.14681464X-RAY DIFFRACTION99.44
1.97-2.170.18151470.15341466X-RAY DIFFRACTION99.81
2.17-2.490.18251480.16481474X-RAY DIFFRACTION99.82
2.49-3.130.19291530.17671498X-RAY DIFFRACTION99.82
3.13-32.810.19691470.18351473X-RAY DIFFRACTION93.21
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)
10.7944891964150.518722726168-0.3882937500730.7845509712660.2497040944830.764272371465-0.0505068683077-0.0409916844028-0.170846153366-0.01379617707220.09646407308270.1348071190340.158048276198-0.1154943223365.3783392969E-60.1254062399530.0008417134717920.01509253931780.1094033765090.0133503137070.13322190555712.82792787164.7213850648723.623627316
21.46471250024-0.1035095873520.02333377765611.372571691041.093782494760.957150794537-0.0486441475315-0.116666187587-0.006154818555660.2380775486960.0810675339575-0.0122915123397-0.1134995613390.06545860354790.007004965619970.0775953976262-0.003600995212650.004523813448460.09553666601810.003394134228290.076174087738614.87214183878.2146312655225.9565700287
30.682037090715-0.005307235385590.004347992430130.6795271987810.3120034139010.1386550123850.02178541794820.211630932861-0.0615792752429-0.08378484881360.0816452947426-0.1223202619930.003535789871090.0268120014240.0002751448259210.0966689699152-0.01174143100990.003841904642570.114512980957-0.01277370708810.079458830368921.454779986.4249520854419.0974506166
40.381493376905-0.1032521410630.04302448719040.465039398361-0.2028517950710.515671911775-0.004092953934650.2774273282210.0543946567962-0.5984474580660.176226650638-0.0233912107639-0.09395799249650.365121194936-0.0002239765867690.213419986372-0.01114188003330.0165408544630.176698670203-0.01514022866120.14737908769823.88673289573.284335912034.36725593059
50.1974339337570.0774040061949-0.02467254284030.2882562823330.06809928643030.0437943731017-0.06843330578080.0666208070730.0662732336073-0.01290384378090.154896801293-0.152916342136-0.1128226190290.1452871683313.32240433044E-60.125270607205-0.008663603389940.003190686213870.133659479267-0.02165284846980.111253143723.528455085911.208109879622.0992161372
61.31775267976-0.37849365926-0.5269616646851.66504309627-0.1279308140840.347917493808-0.006431258707950.02749802351350.134827736973-0.08116955454740.0511409283885-0.0779356068992-0.04764535446640.002944460712132.7412883436E-70.08526268768-0.02276809467370.007163218238480.08712248183890.003374594127880.089781776296916.612698731110.715824945318.036329542
70.1630565369970.08286553191840.03459338969720.07625837277660.02142534901760.006014101748330.09704825846060.092887987383-0.4817317334070.04675233774240.0495257565401-0.3216185202670.1847638481630.1379439504880.0005854934938260.1447535408390.0106855338895-0.03476479250920.124289277463-0.002437808653950.23056659771524.284191076-1.7024457573125.1606436791
80.1237506756090.0281024584425-0.01310152531440.148610594910.1181721685260.1075892847170.04070163008920.207581633686-0.00721534521489-0.3158209108930.1349503471980.500542777252-0.0540608502102-0.134748742038-1.15020566679E-50.166425316116-0.00172460573673-0.01525416353770.164926676130.02961972345790.14010247349.906982023510.143843183710.1288229196
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 708 through 721 )708 - 7211 - 14
22chain 'A' and (resid 722 through 742 )722 - 74215 - 28
33chain 'A' and (resid 743 through 750 )743 - 75029 - 36
44chain 'A' and (resid 751 through 762 )751 - 76237 - 47
55chain 'A' and (resid 763 through 768 )763 - 76848 - 55
66chain 'A' and (resid 769 through 790 )769 - 79056 - 79
77chain 'A' and (resid 791 through 802 )791 - 80280 - 93
88chain 'A' and (resid 803 through 810 )803 - 81094 - 103

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