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- PDB-6j6u: Rat PTPRZ D1-D2 domain -

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Basic information

Entry
Database: PDB / ID: 6j6u
TitleRat PTPRZ D1-D2 domain
ComponentsReceptor-type tyrosine-protein phosphatase zeta
KeywordsHYDROLASE / Protein Tyrosine Phosphatase
Function / homology
Function and homology information


MDK and PTN in ALK signaling / perineuronal net / regulation of oligodendrocyte progenitor proliferation / negative regulation of dendrite development / Other interleukin signaling / positive regulation of Schwann cell migration / positive regulation of neuron migration / axonal fasciculation / positive regulation of dendrite development / regulation of myelination ...MDK and PTN in ALK signaling / perineuronal net / regulation of oligodendrocyte progenitor proliferation / negative regulation of dendrite development / Other interleukin signaling / positive regulation of Schwann cell migration / positive regulation of neuron migration / axonal fasciculation / positive regulation of dendrite development / regulation of myelination / positive regulation of peptidyl-tyrosine phosphorylation / regulation of dendrite morphogenesis / fibroblast growth factor binding / peptidyl-tyrosine dephosphorylation / phosphatase activity / oligodendrocyte differentiation / positive regulation of oligodendrocyte differentiation / negative regulation of cell-substrate adhesion / neuron development / hematopoietic progenitor cell differentiation / protein-tyrosine-phosphatase / extracellular matrix / axonogenesis / protein tyrosine phosphatase activity / filopodium / hippocampus development / positive regulation of neuron projection development / postsynaptic density membrane / visual learning / integrin binding / ruffle membrane / positive regulation of fibroblast proliferation / lamellipodium / growth cone / dendritic spine / negative regulation of neuron apoptotic process / postsynaptic membrane / learning or memory / positive regulation of cell migration / axon / negative regulation of cell population proliferation / neuronal cell body / synapse / dendrite / glutamatergic synapse / extracellular space / plasma membrane
Similarity search - Function
Receptor-type tyrosine-protein phosphatase, carbonic anhydrase domain / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 ...Receptor-type tyrosine-protein phosphatase, carbonic anhydrase domain / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 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 / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase zeta
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.32 Å
AuthorsSugawara, H.
Citation
Journal: J.Biol.Chem. / Year: 2019
Title: A head-to-toe dimerization has physiological relevance for ligand-induced inactivation of protein tyrosine receptor type Z.
Authors: Fujikawa, A. / Sugawara, H. / Tanga, N. / Ishii, K. / Kuboyama, K. / Uchiyama, S. / Suzuki, R. / Noda, M.
#1: Journal: Scientific Reports / Year: 2016
Title: Small-molecule inhibition of PTPRZ suppresses tumor growth in a rat model of glioblastoma.
Authors: Fujikawa, A. / Nagahira, A. / Sugawara, H. / Ishii, K. / Imajo, S. / Matsumoto, M. / Kuboyama, K. / Suzuki, R. / Tanga, N. / Noda, M. / Uchiyama, S. / Tomoo, T. / Ogata, A. / Masumura, M. / Noda, M.
#2: Journal: Sci Rep / Year: 2017
Title: Targeting PTPRZ inhibits stem cell-like properties and tumorigenicity in glioblastoma cells.
Authors: Fujikawa, A. / Sugawara, H. / Tanaka, T. / Matsumoto, M. / Kuboyama, K. / Suzuki, R. / Tanga, N. / Ogata, A. / Masumura, M. / Noda, M.
History
DepositionJan 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Receptor-type tyrosine-protein phosphatase zeta
B: Receptor-type tyrosine-protein phosphatase zeta


Theoretical massNumber of molelcules
Total (without water)141,1292
Polymers141,1292
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-5 kcal/mol
Surface area45600 Å2
Unit cell
Length a, b, c (Å)127.725, 147.585, 65.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 1699 - 2285 / Label seq-ID: 1 - 587

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Receptor-type tyrosine-protein phosphatase zeta / R-PTP-zeta


Mass: 70564.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ptprz1, Ptprz, Ptpz / Production host: Bombyx mori (domestic silkworm) / References: UniProt: Q62656, protein-tyrosine-phosphatase

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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: 2.19 Å3/Da / Density % sol: 43.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 14% PEG3350, 0.15M potassium fluoride, bis-Tris propane pH6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.32→100 Å / Num. obs: 15767 / % possible obs: 84 % / Redundancy: 3.3 % / Net I/σ(I): 13
Reflection shellResolution: 3.32→3.41 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NLK

2nlk


Resolution: 3.32→38.97 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.823 / SU B: 29.021 / SU ML: 0.49 / Cross valid method: THROUGHOUT / ESU R Free: 0.183 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31787 859 5.4 %RANDOM
Rwork0.23464 ---
obs0.23925 14903 83.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 82.573 Å2
Baniso -1Baniso -2Baniso -3
1-56.87 Å20 Å20 Å2
2---29.68 Å20 Å2
3----27.19 Å2
Refinement stepCycle: 1 / Resolution: 3.32→38.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8547 0 0 0 8547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198744
X-RAY DIFFRACTIONr_bond_other_d0.0020.027945
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.93511849
X-RAY DIFFRACTIONr_angle_other_deg0.993318455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2651029
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02524.378434
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.645151516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6021544
X-RAY DIFFRACTIONr_chiral_restr0.0810.21317
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219549
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021767
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.828.3454173
X-RAY DIFFRACTIONr_mcbond_other5.828.3454172
X-RAY DIFFRACTIONr_mcangle_it9.33912.55183
X-RAY DIFFRACTIONr_mcangle_other9.33812.55184
X-RAY DIFFRACTIONr_scbond_it4.9788.5794571
X-RAY DIFFRACTIONr_scbond_other4.9788.5794572
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.21512.7446667
X-RAY DIFFRACTIONr_long_range_B_refined13.43196.9319846
X-RAY DIFFRACTIONr_long_range_B_other13.4396.9359847
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 33606 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.325→3.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 55 -
Rwork0.358 907 -
obs--70.94 %

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