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- PDB-3lnx: Second PDZ domain from human PTP1E -

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Basic information

Entry
Database: PDB / ID: 3lnx
TitleSecond PDZ domain from human PTP1E
ComponentsTyrosine-protein phosphatase non-receptor type 13
KeywordsSIGNALING PROTEIN / PDZ2 / Structural Genomics / Protein Structure Initiative / PSI-2 / Center for Eukaryotic Structural Genomics / CESG / Cytoskeleton
Function / homology
Function and homology information


negative regulation of excitatory synapse assembly / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / phosphatidylinositol 3-kinase regulatory subunit binding / cellular response to toxic substance / Interleukin-37 signaling / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / Synthesis of PIPs at the plasma membrane / peptidyl-tyrosine dephosphorylation ...negative regulation of excitatory synapse assembly / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / phosphatidylinositol 3-kinase regulatory subunit binding / cellular response to toxic substance / Interleukin-37 signaling / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / Synthesis of PIPs at the plasma membrane / peptidyl-tyrosine dephosphorylation / negative regulation of protein phosphorylation / protein dephosphorylation / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / lamellipodium / cell body / cytoskeleton / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Tyrosine-protein phosphatase non-receptor type 13 / Unstructured linker region on PTN13 protein between PDZ / : / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal ...Tyrosine-protein phosphatase non-receptor type 13 / Unstructured linker region on PTN13 protein between PDZ / : / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / PDZ domain / Pdz3 Domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Protein tyrosine phosphatase, catalytic 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 domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / THIOCYANATE ION / Tyrosine-protein phosphatase non-receptor type 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.642 Å
AuthorsZhang, J. / Chang, A. / Ke, H. / Phillips Jr., G.N. / Lee, A.L. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Biochemistry / Year: 2010
Title: Crystallographic and nuclear magnetic resonance evaluation of the impact of peptide binding to the second PDZ domain of protein tyrosine phosphatase 1E.
Authors: Zhang, J. / Sapienza, P.J. / Ke, H. / Chang, A. / Hengel, S.R. / Wang, H. / Phillips, G.N. / Lee, A.L.
History
DepositionFeb 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 13
B: Tyrosine-protein phosphatase non-receptor type 13
C: Tyrosine-protein phosphatase non-receptor type 13
D: Tyrosine-protein phosphatase non-receptor type 13
E: Tyrosine-protein phosphatase non-receptor type 13
F: Tyrosine-protein phosphatase non-receptor type 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,10745
Polymers60,1226
Non-polymers3,98639
Water7,800433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.023, 95.148, 101.989
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Tyrosine-protein phosphatase non-receptor type 13 / Protein-tyrosine phosphatase 1E / PTP-E1 / hPTPE1 / PTP-BAS / Protein-tyrosine phosphatase PTPL1 / ...Protein-tyrosine phosphatase 1E / PTP-E1 / hPTPE1 / PTP-BAS / Protein-tyrosine phosphatase PTPL1 / Fas-associated protein-tyrosine phosphatase 1 / FAP-1


Mass: 10020.252 Da / Num. of mol.: 6 / Fragment: PDZ2 domain
Source method: isolated from a genetically manipulated source
Details: NdeI BamHI restriction sites / Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN13, PNP1, PTP1E, PTPL1 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12923
#2: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / 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: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 28% PEG 3350, 0.2 M KI, 0.2 M NaSCN, 0.1 M NaAc, pH 4.5, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A11.0809
SYNCHROTRONNSLS X29A21.0809
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2007
Radiation
IDMonochromatorProtocolScattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHx-ray1
2Si(111)SINGLE WAVELENGTHx-ray1
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.642→50 Å / Num. obs: 74902 / % possible obs: 98.6 % / Redundancy: 16.2 % / Rmerge(I) obs: 0.114 / Χ2: 0.704 / Net I/σ(I): 12.8
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.856 / Num. unique all: 2764 / Χ2: 0.782 / % possible all: 73.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.642→39.643 Å / Occupancy max: 1 / Occupancy min: 0.31 / SU ML: 0.2 / σ(F): 0.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.237 3545 2.66 %
Rwork0.196 --
obs0.197 69477 92.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.995 Å2 / ksol: 0.324 e/Å3
Displacement parametersBiso max: 144.03 Å2 / Biso mean: 38.951 Å2 / Biso min: 13.16 Å2
Baniso -1Baniso -2Baniso -3
1-13.051 Å2-0 Å2-0 Å2
2---4.491 Å20 Å2
3----7.576 Å2
Refinement stepCycle: LAST / Resolution: 1.642→39.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4140 0 67 433 4640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084246
X-RAY DIFFRACTIONf_angle_d1.1815710
X-RAY DIFFRACTIONf_chiral_restr0.08670
X-RAY DIFFRACTIONf_plane_restr0.004751
X-RAY DIFFRACTIONf_dihedral_angle_d15.2421546
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.642-1.6650.3151040.2823538364263
1.665-1.6890.2581060.2564381448778
1.689-1.7140.2971310.244606473782
1.714-1.7410.3081220.2294786490885
1.741-1.7690.2521350.2174793492886
1.769-1.80.2391250.2145028515388
1.8-1.8320.2441280.2035010513889
1.832-1.8680.2321380.2035090522890
1.868-1.9060.2691310.2045151528291
1.906-1.9470.1931490.1915288543795
1.947-1.9920.2051490.1885321547094
1.992-2.0420.1961570.1915413557096
2.042-2.0980.2751560.2055439559597
2.098-2.1590.2421490.1915475562498
2.159-2.2290.2211330.1935492562597
2.229-2.3090.2241640.1915481564598
2.309-2.4010.2921360.2065522565897
2.401-2.510.2641530.1975357551095
2.51-2.6430.2841500.2015358550896
2.643-2.8080.221530.2085465561897
2.808-3.0250.2091480.2065508565698
3.025-3.3290.2551590.1945563572299
3.329-3.8110.2281610.185584574599
3.811-4.80.2081530.15756305783100
4.8-39.6540.2211550.1955576573199

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