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- PDB-1lar: CRYSTAL STRUCTURE OF THE TANDEM PHOSPHATASE DOMAINS OF RPTP LAR -

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Basic information

Entry
Database: PDB / ID: 1lar
TitleCRYSTAL STRUCTURE OF THE TANDEM PHOSPHATASE DOMAINS OF RPTP LAR
ComponentsPROTEIN (LAR)
KeywordsHYDROLASE / TYROSINE PHOSPHATEASE / LAR PROTEIN
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 / synaptic membrane adhesion / transmembrane receptor protein tyrosine phosphatase activity / Synaptic adhesion-like molecules / regulation of axon regeneration / peptidyl-tyrosine dephosphorylation / Insulin receptor recycling ...chondroitin sulfate proteoglycan binding / cell surface receptor protein tyrosine phosphatase signaling pathway / neuron projection regeneration / Receptor-type tyrosine-protein phosphatases / synaptic membrane adhesion / transmembrane receptor protein tyrosine phosphatase activity / Synaptic adhesion-like molecules / regulation of axon regeneration / peptidyl-tyrosine dephosphorylation / Insulin receptor recycling / cell adhesion molecule binding / protein-tyrosine-phosphatase / negative regulation of receptor binding / protein tyrosine phosphatase activity / cell migration / heparin binding / cell adhesion / neuron projection / neuronal cell body / protein-containing complex binding / extracellular exosome / plasma membrane
Similarity search - Function
Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / Immunoglobulin I-set / Immunoglobulin I-set 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 ...Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / Immunoglobulin I-set / Immunoglobulin I-set 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 / 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 / Alpha-Beta Complex / Alpha 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 Å
AuthorsNam, H.-J. / Poy, F. / Krueger, N. / Saito, H. / Frederick, C.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Crystal structure of the tandem phosphatase domains of RPTP LAR.
Authors: Nam, H.J. / Poy, F. / Krueger, N.X. / Saito, H. / Frederick, C.A.
History
DepositionApr 20, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 25, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Aug 16, 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: PROTEIN (LAR)
B: PROTEIN (LAR)


Theoretical massNumber of molelcules
Total (without water)132,1842
Polymers132,1842
Non-polymers00
Water8,521473
1
A: PROTEIN (LAR)


Theoretical massNumber of molelcules
Total (without water)66,0921
Polymers66,0921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (LAR)


Theoretical massNumber of molelcules
Total (without water)66,0921
Polymers66,0921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.920, 62.730, 161.590
Angle α, β, γ (deg.)90.00, 98.94, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999298, -0.034489, 0.014624), (-0.033924, 0.998731, 0.037229), (-0.015889, 0.036707, -0.9992)
Vector: 60.8246, 25.6288, 239.7623)

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Components

#1: Protein PROTEIN (LAR)


Mass: 66092.094 Da / Num. of mol.: 2 / Fragment: PHOSPHATASE / Mutation: P1307M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P10586, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 2.53 Å3/Da / Density % sol: 51.45 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
2100 mMTris-HCl1drop
38-16 %(w/v)PEG80001drop
40.2 M1dropLi2SO4

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91
DetectorDetector: CCD / Date: Dec 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 81312 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 7
Reflection
*PLUS
Num. measured all: 267242

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.8refinement
MOSFLMdata reduction
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YFO

1yfo


Resolution: 2→50 Å / Cross valid method: THROUGHTOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.274 -5 %RANDOM
Rwork0.222 ---
obs-81312 90.7 %-
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8869 0 0 473 9342
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.33
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS

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