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- PDB-4bjo: Nitrate in the active site of PTP1b is a putative mimetic of the ... -

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Basic information

Entry
Database: PDB / ID: 4bjo
TitleNitrate in the active site of PTP1b is a putative mimetic of the transition state
ComponentsTYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 1
KeywordsHYDROLASE / PHOSPHATASE / TRANSITION STATE / QUANTUM CHEMISTRY
Function / homology
Function and homology information


PTK6 Down-Regulation / regulation of hepatocyte growth factor receptor signaling pathway / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / positive regulation of protein tyrosine kinase activity / IRE1-mediated unfolded protein response / mitochondrial crista / platelet-derived growth factor receptor-beta signaling pathway ...PTK6 Down-Regulation / regulation of hepatocyte growth factor receptor signaling pathway / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / positive regulation of protein tyrosine kinase activity / IRE1-mediated unfolded protein response / mitochondrial crista / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / cytoplasmic side of endoplasmic reticulum membrane / negative regulation of vascular associated smooth muscle cell migration / positive regulation of IRE1-mediated unfolded protein response / regulation of type I interferon-mediated signaling pathway / negative regulation of PERK-mediated unfolded protein response / positive regulation of systemic arterial blood pressure / vascular endothelial cell response to oscillatory fluid shear stress / regulation of endocytosis / Regulation of IFNA/IFNB signaling / peptidyl-tyrosine dephosphorylation / regulation of postsynapse assembly / regulation of proteolysis / positive regulation of JUN kinase activity / cellular response to fibroblast growth factor stimulus / growth hormone receptor signaling pathway via JAK-STAT / cellular response to angiotensin / positive regulation of endothelial cell apoptotic process / negative regulation of cell-substrate adhesion / negative regulation of MAP kinase activity / cellular response to unfolded protein / regulation of signal transduction / negative regulation of signal transduction / Regulation of IFNG signaling / Growth hormone receptor signaling / positive regulation of heart rate / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / endoplasmic reticulum unfolded protein response / positive regulation of cardiac muscle cell apoptotic process / MECP2 regulates neuronal receptors and channels / protein dephosphorylation / Insulin receptor recycling / cellular response to platelet-derived growth factor stimulus / ephrin receptor binding / Integrin signaling / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / negative regulation of insulin receptor signaling pathway / cellular response to nitric oxide / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein phosphatase 2A binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / endosome lumen / insulin receptor binding / cellular response to nerve growth factor stimulus / response to nutrient levels / negative regulation of ERK1 and ERK2 cascade / Negative regulation of MET activity / receptor tyrosine kinase binding / insulin receptor signaling pathway / negative regulation of neuron projection development / actin cytoskeleton organization / cellular response to hypoxia / early endosome / postsynapse / mitochondrial matrix / cadherin binding / negative regulation of cell population proliferation / protein kinase binding / glutamatergic synapse / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-1/2 / : / 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 ...Protein-tyrosine phosphatase, non-receptor type-1/2 / : / 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 / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsKenny, P.W. / Newman, J. / Peat, T.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Nitrate in the Active Site of Protein Tyrosine Phosphatase 1B is a Putative Mimetic of the Transition State.
Authors: Kenny, P.W. / Newman, J. / Peat, T.S.
History
DepositionApr 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 / _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 1
B: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,07411
Polymers78,6972
Non-polymers3779
Water2,234124
1
A: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5927
Polymers39,3491
Non-polymers2446
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4824
Polymers39,3491
Non-polymers1333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)161.620, 66.765, 68.771
Angle α, β, γ (deg.)90.00, 95.01, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: -5 - 280 / Label seq-ID: 12 - 297

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

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 1 / PTP1B PROTEIN PHOSPHATASE / PROTEIN-TYROSINE PHOSPHATASE 1B


Mass: 39348.691 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 2-321
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P18031, protein-tyrosine-phosphatase

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Non-polymers , 5 types, 133 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsHIS-TAG AT N-TERMINUS

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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: 2.79 Å3/Da / Density % sol: 55.9 % / Description: NONE
Crystal growTemperature: 281 K / pH: 8.1
Details: 100 MM HEPES PH 8.1, 25.4% PEG 4000, 225 MM MGNO3 AT 281K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1.033
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 16, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.06→80.5 Å / Num. obs: 44854 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.6
Reflection shellResolution: 2.06→2.17 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.6 / % possible all: 93.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AJ5

3aj5


Resolution: 2.06→68.6 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.475 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23932 2290 5.1 %RANDOM
Rwork0.21529 ---
obs0.21652 42525 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.386 Å2
Baniso -1Baniso -2Baniso -3
1--2.19 Å20 Å20.07 Å2
2--2.15 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.06→68.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4671 0 18 124 4813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194846
X-RAY DIFFRACTIONr_bond_other_d0.0030.024582
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.9566527
X-RAY DIFFRACTIONr_angle_other_deg0.901310578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6375578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5323.875240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.56715897
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4251535
X-RAY DIFFRACTIONr_chiral_restr0.0680.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215433
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021146
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_it3.8536.3042306
X-RAY DIFFRACTIONr_mcbond_other3.8516.3022305
X-RAY DIFFRACTIONr_mcangle_it5.39410.6052886
X-RAY DIFFRACTIONr_mcangle_other5.39410.6082887
X-RAY DIFFRACTIONr_scbond_it4.0786.8392539
X-RAY DIFFRACTIONr_scbond_other4.0766.8392539
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.25711.2953642
X-RAY DIFFRACTIONr_long_range_B_refined8.15633.685569
X-RAY DIFFRACTIONr_long_range_B_other8.15533.6815570
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 17493 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.06→2.113 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 179 -
Rwork0.334 2764 -
obs--89.32 %

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