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- PDB-5awx: Crystal structure of Human PTPRZ D1 domain -

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Basic information

Entry
Database: PDB / ID: 5awx
TitleCrystal structure of Human PTPRZ D1 domain
ComponentsReceptor-type tyrosine-protein phosphatase zeta
KeywordsHYDROLASE / Protein Tyrosine Phosphatase
Function / homology
Function and homology information


perineuronal net / regulation of oligodendrocyte progenitor proliferation / MDK and PTN in ALK signaling / transmembrane receptor protein tyrosine phosphatase activity / protein dephosphorylation / regulation of myelination / Other interleukin signaling / peptidyl-tyrosine dephosphorylation / oligodendrocyte differentiation / positive regulation of oligodendrocyte differentiation ...perineuronal net / regulation of oligodendrocyte progenitor proliferation / MDK and PTN in ALK signaling / transmembrane receptor protein tyrosine phosphatase activity / protein dephosphorylation / regulation of myelination / Other interleukin signaling / peptidyl-tyrosine dephosphorylation / oligodendrocyte differentiation / positive regulation of oligodendrocyte differentiation / hematopoietic progenitor cell differentiation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / axonogenesis / central nervous system development / integrin binding / neuron projection development / negative regulation of neuron apoptotic process / learning or memory / synapse / signal transduction / extracellular region / 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
BROMIDE ION / Receptor-type tyrosine-protein phosphatase zeta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsSugawara, H.
CitationJournal: Sci Rep / Year: 2016
Title: Small-molecule inhibition of PTPRZ reduces 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.
History
DepositionJul 10, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Receptor-type tyrosine-protein phosphatase zeta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2745
Polymers33,9541
Non-polymers3204
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-1 kcal/mol
Surface area13290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.641, 72.245, 90.557
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Receptor-type tyrosine-protein phosphatase zeta / R-PTP-zeta / Protein-tyrosine phosphatase receptor type Z polypeptide 1 / Protein-tyrosine ...R-PTP-zeta / Protein-tyrosine phosphatase receptor type Z polypeptide 1 / Protein-tyrosine phosphatase receptor type Z polypeptide 2 / R-PTP-zeta-2


Mass: 33954.402 Da / Num. of mol.: 1 / Fragment: UNP residues 1698-1993
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRZ1, HTPZP2, PTPRZ, PTPRZ2, PTPZ / Production host: Bombyx mori (domestic silkworm) / References: UniProt: P23471, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE CORRESPONDS TO THE ISOFORM 2 FOUND IN UNP P23471.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10% (w/v) PEG8000, 20% (v/v) ethylene glycol, 30mM sodium fluoride, 30mM sodium bromide, 30mM sodium iodide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→31.4 Å / Num. obs: 29084 / % possible obs: 99.5 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 45.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QCB

3qcb


Resolution: 1.86→31.4 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.879 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22094 1547 5.1 %RANDOM
Rwork0.18563 ---
obs0.18745 29084 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.281 Å2
Baniso -1Baniso -2Baniso -3
1--2.27 Å20 Å20 Å2
2---0.2 Å20 Å2
3---2.47 Å2
Refinement stepCycle: 1 / Resolution: 1.86→31.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2280 0 4 247 2531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192347
X-RAY DIFFRACTIONr_bond_other_d0.0020.022204
X-RAY DIFFRACTIONr_angle_refined_deg1.9771.9283190
X-RAY DIFFRACTIONr_angle_other_deg1.00635053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7185284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47723.846117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34915387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5451514
X-RAY DIFFRACTIONr_chiral_restr0.1640.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022671
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02577
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_it1.6511.4691133
X-RAY DIFFRACTIONr_mcbond_other1.6211.4671132
X-RAY DIFFRACTIONr_mcangle_it2.3072.191412
X-RAY DIFFRACTIONr_mcangle_other2.3082.1911413
X-RAY DIFFRACTIONr_scbond_it2.4361.7331214
X-RAY DIFFRACTIONr_scbond_other2.4361.7331214
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7432.4931777
X-RAY DIFFRACTIONr_long_range_B_refined5.80313.142865
X-RAY DIFFRACTIONr_long_range_B_other5.62212.6242764
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 128 -
Rwork0.331 2045 -
obs--97.88 %
Refinement TLS params.Method: refined / Origin x: 20.0556 Å / Origin y: -0.7811 Å / Origin z: 1.1515 Å
111213212223313233
T0.0285 Å20.0109 Å20.0051 Å2-0.0049 Å20.0014 Å2--0.0093 Å2
L0.7114 °20.1783 °20.0472 °2-0.9363 °20.2243 °2--0.6419 °2
S0.0205 Å °0.0128 Å °0.0605 Å °-0.0122 Å °-0.0008 Å °0.0533 Å °-0.1081 Å °-0.0316 Å °-0.0197 Å °

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