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- PDB-2i4g: Structural studies of protein tyrosine phosphatase beta catalytic... -

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Basic information

Entry
Database: PDB / ID: 2i4g
TitleStructural studies of protein tyrosine phosphatase beta catalytic domain in complex with a sulfamic acid (soaking experiment)
ComponentsReceptor-type tyrosine-protein phosphatase beta
KeywordsHYDROLASE / protein tyrosine phosphatase / WPD-loop / sulfamic acid / phosphatase / inhibitor / drug design
Function / homology
Function and homology information


glial cell migration / transmembrane receptor protein tyrosine phosphatase activity / phosphate-containing compound metabolic process / dephosphorylation / tertiary granule membrane / specific granule membrane / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity ...glial cell migration / transmembrane receptor protein tyrosine phosphatase activity / phosphate-containing compound metabolic process / dephosphorylation / tertiary granule membrane / specific granule membrane / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / osteoblast differentiation / angiogenesis / receptor complex / cadherin binding / Neutrophil degranulation / plasma membrane
Similarity search - Function
PTPRJ, transmembrane domain / TM proximal of protein tyrosine phosphatase, receptor type J / : / 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 ...PTPRJ, transmembrane domain / TM proximal of protein tyrosine phosphatase, receptor type J / : / 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 / Fibronectin type III domain / 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
Chem-UA1 / Receptor-type tyrosine-protein phosphatase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsEvdokimov, A.G. / Pokross, M.E. / Walter, R.L. / Mekel, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Engineering the catalytic domain of human protein tyrosine phosphatase beta for structure-based drug discovery.
Authors: Evdokimov, A.G. / Pokross, M. / Walter, R. / Mekel, M. / Cox, B. / Li, C. / Bechard, R. / Genbauffe, F. / Andrews, R. / Diven, C. / Howard, B. / Rastogi, V. / Gray, J. / Maier, M. / Peters, K.G.
History
DepositionAug 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,8603
Polymers36,2881
Non-polymers5722
Water4,486249
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.852, 69.610, 117.777
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 beta / Protein-tyrosine phosphatase beta / R-PTP-beta


Mass: 36288.035 Da / Num. of mol.: 1 / Fragment: catalytic domain, residues 1662-1973
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRB, PTPB / Plasmid: pDEST-HisMBP / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: P23467, protein-tyrosine-phosphatase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-UA1 / N-(TERT-BUTOXYCARBONYL)-L-TYROSYL-N-METHYL-4-(SULFOAMINO)-L-PHENYLALANINAMIDE


Mass: 536.598 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H32N4O8S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.19 Å3/Da / Density % sol: 43.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: 20% PEG 8000, 200 mM MgCl2, 80 mM NH4OAc, 1% BME, 0.1% BOG, 5mM DTT, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 2, 2005 / Details: Si monochromator
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→34.2 Å / Num. all: 29360 / Num. obs: 29360 / % possible obs: 73.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 22.77 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 15.1
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3 / % possible all: 39.3

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2I4E

2i4e


Resolution: 1.65→34.2 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.533 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.129 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1467 5 %RANDOM
Rwork0.176 ---
all0.178 29349 --
obs0.17 29349 74.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.874 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.47 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.65→34.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 38 249 2649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222495
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.9583387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2735295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.93123.438128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66515437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.781522
X-RAY DIFFRACTIONr_chiral_restr0.1260.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021915
X-RAY DIFFRACTIONr_nbd_refined0.2330.21226
X-RAY DIFFRACTIONr_nbtor_refined0.3220.21725
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.350.214
X-RAY DIFFRACTIONr_mcbond_it1.5471.51479
X-RAY DIFFRACTIONr_mcangle_it2.27522372
X-RAY DIFFRACTIONr_scbond_it3.54931141
X-RAY DIFFRACTIONr_scangle_it5.2254.51011
LS refinement shellResolution: 1.646→1.688 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 33 -
Rwork0.212 624 -
obs-657 22.75 %
Refinement TLS params.Method: refined / Details: Chain A / Origin x: 2.306 Å / Origin y: 21.38 Å / Origin z: 15.59 Å
111213212223313233
T-0.0085 Å2-0.0119 Å2-0.0007 Å2--0.0233 Å20.0029 Å2--0.0026 Å2
L0.1483 °2-0.0875 °2-0.0823 °2-0.1493 °2-0.0618 °2--0.31 °2
S-0.0071 Å °-0.0106 Å °0.0084 Å °0.008 Å °0.0033 Å °-0.0106 Å °-0.037 Å °0.0115 Å °0.0039 Å °
Refinement TLS groupSelection: ALL

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