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- PDB-2bzl: CRYSTAL STRUCTURE OF THE HUMAN PROTEIN TYROSINE PHOSPHATASE N14 A... -

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Basic information

Entry
Database: PDB / ID: 2bzl
TitleCRYSTAL STRUCTURE OF THE HUMAN PROTEIN TYROSINE PHOSPHATASE N14 AT 1. 65 A RESOLUTION
ComponentsTYROSINE-PROTEIN PHOSPHATASE, NON-RECEPTOR TYPE 14
KeywordsHYDROLASE / PTPN14 / PROTEIN PHOSPHATASE
Function / homology
Function and homology information


lymphangiogenesis / regulation of protein export from nucleus / Interleukin-37 signaling / 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 / transcription coregulator activity ...lymphangiogenesis / regulation of protein export from nucleus / Interleukin-37 signaling / 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 / transcription coregulator activity / receptor tyrosine kinase binding / cytoskeleton / negative regulation of cell population proliferation / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-14/21 / PTPN14/21, FERM domain C-lobe / 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 domain signature 1. / FERM conserved site / FERM domain signature 2. ...Protein-tyrosine phosphatase, non-receptor type-14/21 / PTPN14/21, FERM domain C-lobe / 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 domain signature 1. / FERM conserved site / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / Protein tyrosine phosphatase superfamily / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / 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 / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / PH-like domain superfamily / Ubiquitin-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 14
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsDebreczeni, J.E. / Barr, A. / Eswaran, J. / Das, S. / Burgess, N. / Longman, E. / Fedorov, O. / Gileadi, O. / von Delft, F. / Sundstrom, M. ...Debreczeni, J.E. / Barr, A. / Eswaran, J. / Das, S. / Burgess, N. / Longman, E. / Fedorov, O. / Gileadi, O. / von Delft, F. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Knapp, S.
CitationJournal: Proteins / Year: 2006
Title: Crystal Structure of Human Protein Tyrosine Phosphatase 14 (Ptpn14) at 1.65-A Resolution.
Authors: Barr, A.J. / Debreczeni, J.E. / Eswaran, J. / Knapp, S.
History
DepositionAug 18, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / struct_biol
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.5May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.6Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TYROSINE-PROTEIN PHOSPHATASE, NON-RECEPTOR TYPE 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9385
Polymers37,6221
Non-polymers3164
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)87.636, 87.636, 77.115
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein TYROSINE-PROTEIN PHOSPHATASE, NON-RECEPTOR TYPE 14 / PROTEIN-TYROSINE PHOSPHATASE PEZ


Mass: 37622.031 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 886-1187
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PLIC SGC / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q15678, protein-tyrosine-phosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O
Compound detailsBELONGS TO THE PROTEIN-TYROSINE PHOSPHATASE FAMILY. NON-RECEPTOR CLASS SUBFAMILY.
Sequence detailsRESIDUES 886-1187 CORRESPOND TO THE CATALYTIC DOMAIN OF OF THE PROTEIN, RESIDUES 863-885 ARE PART ...RESIDUES 886-1187 CORRESPOND TO THE CATALYTIC DOMAIN OF OF THE PROTEIN, RESIDUES 863-885 ARE PART OF A EXPRESSION SYSTEM HIS-TAG.

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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: 2.4 Å3/Da / Density % sol: 49.2 %
Crystal growMethod: vapor diffusion, sitting drop
Details: SITTING DROP, 20% PEG3350, 0.2 M LI2SO4, 0.1 M BIS TRIS PROPANE PH 6.5, CRYO 20% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.008
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 2, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 41374 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 6.73 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.08
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.05 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FPR

1fpr


Resolution: 1.65→77.15 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.067 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1820 4.4 %RANDOM
Rwork0.185 ---
obs0.186 39553 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20.18 Å20 Å2
2--0.36 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.65→77.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2235 0 18 244 2497
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212348
X-RAY DIFFRACTIONr_bond_other_d0.0010.022109
X-RAY DIFFRACTIONr_angle_refined_deg1.1671.9393195
X-RAY DIFFRACTIONr_angle_other_deg0.72834880
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0185295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.42223.301103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08515385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9831514
X-RAY DIFFRACTIONr_chiral_restr0.0720.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022594
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02486
X-RAY DIFFRACTIONr_nbd_refined0.2070.2450
X-RAY DIFFRACTIONr_nbd_other0.1870.22068
X-RAY DIFFRACTIONr_nbtor_refined0.180.21139
X-RAY DIFFRACTIONr_nbtor_other0.0810.21280
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2199
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1850.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8931.51454
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.42422325
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.45431004
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0914.5863
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.308 127
Rwork0.25 2845

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