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- PDB-3hqc: Crystal structure of Phosphotyrosine-binding domain from the Huma... -

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Basic information

Entry
Database: PDB / ID: 3hqc
TitleCrystal structure of Phosphotyrosine-binding domain from the Human Tensin-like C1 domain-containing phosphatase (TENC1)
ComponentsTensin-like C1 domain-containing phosphatase
KeywordsHYDROLASE / Human Tensin-like C1 domain-containing phosphatase / TENC1 / Phosphotyrosine Binding Domain / PTB / TNS2 / KIAA1075 / STRUCTURAL GENOMICS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / NEW YORK SGX Research Center for Structural Genomics / NYSGXRC / Cell junction / Cell membrane / Membrane / Metal-binding / Phorbol-ester binding / Phosphoprotein / Protein phosphatase / SH2 domain / Zinc-finger
Function / homology
Function and homology information


multicellular organismal-level homeostasis / collagen metabolic process / cellular homeostasis / response to muscle activity / peptidyl-tyrosine dephosphorylation / negative regulation of insulin receptor signaling pathway / protein-tyrosine-phosphatase / kidney development / protein tyrosine phosphatase activity / multicellular organism growth ...multicellular organismal-level homeostasis / collagen metabolic process / cellular homeostasis / response to muscle activity / peptidyl-tyrosine dephosphorylation / negative regulation of insulin receptor signaling pathway / protein-tyrosine-phosphatase / kidney development / protein tyrosine phosphatase activity / multicellular organism growth / kinase binding / negative regulation of cell population proliferation / focal adhesion / lipid binding / identical protein binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Tensin, phosphotyrosine-binding domain / Tensin-like, SH2 domain / Tensin/EPS8 phosphotyrosine-binding domain / Phosphotyrosine-binding domain / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein ...Tensin, phosphotyrosine-binding domain / Tensin-like, SH2 domain / Tensin/EPS8 phosphotyrosine-binding domain / Phosphotyrosine-binding domain / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / C1-like domain superfamily / PH-domain like / C2 domain superfamily / Protein-tyrosine phosphatase-like / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Tensin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSampathkumar, P. / Romero, R. / Wasserman, S. / Do, J. / Dickey, M. / Bain, K. / Gheyi, T. / Klemke, R. / Atwell, S. / Sauder, J.M. ...Sampathkumar, P. / Romero, R. / Wasserman, S. / Do, J. / Dickey, M. / Bain, K. / Gheyi, T. / Klemke, R. / Atwell, S. / Sauder, J.M. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of Phosphotyrosine-binding domain from the Human Tensin-like C1 domain-containing phosphatase (TENC1)
Authors: Sampathkumar, P. / Romero, R. / Wasserman, S. / Do, J. / Dickey, M. / Bain, K. / Gheyi, T. / Klemke, R. / Atwell, S. / Sauder, J.M. / Burley, S.K.
History
DepositionJun 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tensin-like C1 domain-containing phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8097
Polymers17,3101
Non-polymers4986
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.909, 108.909, 36.196
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Tensin-like C1 domain-containing phosphatase / TENC1 / C1 domain-containing phosphatase and tensin homolog / C1-TEN / Tensin-2


Mass: 17310.248 Da / Num. of mol.: 1
Fragment: Phosphotyrosine Binding Domain, PTB, residues 1264-1409
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA1075, TENC1, TNS2 / Plasmid: BC-pSGX3(BC); modified pET26b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Codon+RIL
References: UniProt: Q63HR2, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 3.58 Å3/Da / Density % sol: 65.64 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 100mM Sodium Acetate pH 4 + 2% Glycerol + 2000mM Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 16, 2009
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→47.14 Å / Num. obs: 23089 / % possible obs: 100 % / Redundancy: 10.9 % / Biso Wilson estimate: 25.92 Å2 / Rsym value: 0.118 / Net I/σ(I): 8.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 3 / Num. unique all: 3337 / Rsym value: 0.637 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Poly-Alanine model of the PDB entry 1WVH

1wvh


Resolution: 1.8→26.16 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 2.5 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.105
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: There are residual postive electron density features which could not be assigned unambigously as protein or buffer components.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1182 5.1 %RANDOM
Rwork0.212 ---
obs0.214 23037 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 79.88 Å2 / Biso mean: 33.104 Å2 / Biso min: 17.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→26.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1040 0 29 79 1148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221180
X-RAY DIFFRACTIONr_bond_other_d0.0040.02751
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.9591640
X-RAY DIFFRACTIONr_angle_other_deg0.8631864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9175168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69624.04347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.7415173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.098156
X-RAY DIFFRACTIONr_chiral_restr0.0870.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021348
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02236
X-RAY DIFFRACTIONr_nbd_refined0.20.2240
X-RAY DIFFRACTIONr_nbd_other0.1990.2758
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2575
X-RAY DIFFRACTIONr_nbtor_other0.0860.2594
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.259
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1190.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2180.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.28
X-RAY DIFFRACTIONr_mcbond_it1.1861.5818
X-RAY DIFFRACTIONr_mcbond_other0.2441.5295
X-RAY DIFFRACTIONr_mcangle_it1.80421238
X-RAY DIFFRACTIONr_scbond_it2.1263456
X-RAY DIFFRACTIONr_scangle_it3.2164.5385
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 81 -
Rwork0.314 1601 -
all-1682 -
obs--100 %

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