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- PDB-3qcm: Human receptor protein tyrosine phosphatase gamma, domain 1, in c... -

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Basic information

Entry
Database: PDB / ID: 3qcm
TitleHuman receptor protein tyrosine phosphatase gamma, domain 1, in complex with 2-[(3,4-dichlorobenzyl)sulfanyl]-4-{[3-({N-[2-(methylamino)ethyl]glycyl}amino)phenyl]ethynyl}benzoic acid
ComponentsReceptor-type tyrosine-protein phosphatase gamma
KeywordsHYDROLASE/HYDROLASE INHIBITOR / TYROSINE RECEPTOR PHOSPHATASE / TWISTED MIXED BETA-SHEETS FLANKED BY {ALPHA}-HELICES / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


negative regulation of epithelial cell migration / transmembrane receptor protein tyrosine phosphatase activity / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cell surface receptor protein tyrosine kinase signaling pathway / negative regulation of neuron projection development / extracellular exosome / identical protein binding / 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 / Tyrosine specific protein phosphatases active site. ...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 / Tyrosine specific protein phosphatases domain profile. / 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
Chem-NXW / Receptor-type tyrosine-protein phosphatase gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSheriff, S.
Citation
Journal: J.Med.Chem. / Year: 2011
Title: Small molecule receptor protein tyrosine phosphatase [gamma](RPTP[gamma]) ligands that inhibit phosphatase activity via perturbation of the tryptophan-proline-aspartate (WPD) loop
Authors: Sheriff, S. / Beno, B.R. / Zhai, W. / Kostich, W.A. / McDonnell, P.A. / Kish, K. / Goldfarb, V. / Gao, M. / Kiefer, S.E. / Yanchunas, J. / Huang, Y. / Shi, S. / Zhu, S. / Dzierba, C. / ...Authors: Sheriff, S. / Beno, B.R. / Zhai, W. / Kostich, W.A. / McDonnell, P.A. / Kish, K. / Goldfarb, V. / Gao, M. / Kiefer, S.E. / Yanchunas, J. / Huang, Y. / Shi, S. / Zhu, S. / Dzierba, C. / Bronson, J. / Macor, J.E. / Appiah, K.K. / Westphal, R.S. / O'Connell, J. / Gerritz, S.W.
#1: Journal: To be Published
Title: Cloning, purification, crystallization and preliminary X-ray analysis of the catalytic domain of human receptor-like protein Tyrosine Phosphatase g in three different crystal forms
Authors: Kish, K. / McDonnell, P.A. / Goldfarb, V. / Gao, M. / Metzler, W.J. / Langley, D.R. / Bryson, J.W. / Kiefer, S.E. / Kostich, W.A. / Carpenter, B. / Westphal, R.S. / Sheriff, S.
History
DepositionJan 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 gamma
B: Receptor-type tyrosine-protein phosphatase gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9476
Polymers71,4712
Non-polymers1,4754
Water1,67593
1
A: Receptor-type tyrosine-protein phosphatase gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4733
Polymers35,7361
Non-polymers7382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Receptor-type tyrosine-protein phosphatase gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4733
Polymers35,7361
Non-polymers7382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.600, 74.600, 81.900
Angle α, β, γ (deg.)90.00, 98.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Receptor-type tyrosine-protein phosphatase gamma / Protein-tyrosine phosphatase gamma / R-PTP-gamma


Mass: 35735.621 Da / Num. of mol.: 2 / Mutation: V948I, S970T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPG, PTPRG / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P23470, protein-tyrosine-phosphatase
#2: Chemical ChemComp-NXW / 2-[(3,4-dichlorobenzyl)sulfanyl]-4-{[3-({N-[2-(methylamino)ethyl]glycyl}amino)phenyl]ethynyl}benzoic acid


Mass: 542.477 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H25Cl2N3O3S
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.52 Å3/Da / Density % sol: 51.21 %
Crystal growTemperature: 277 K / pH: 6.7 / Details: pH 6.7, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 23, 2007 / Details: MICROMAX CONFOCAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 26953 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 51.1 Å2 / Rmerge(I) obs: 0.028 / Net I/σ(I): 43
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 14.6 / % possible all: 93.8

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.9.7refinement
PDB_EXTRACT3.1data extraction
HKL-2000(DENZO)data reduction
HKL-2000(SCALEPACK)data scaling
AMoREphasing
BUSTER2.9.7refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QCD

3qcd


Resolution: 2.4→40.52 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.905 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.36 / SU Rfree Blow DPI: 0.24 / SU Rfree Cruickshank DPI: 0.25
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1034 3.84 %RANDOM
Rwork0.2 ---
obs0.201 26952 96.5 %-
Displacement parametersBiso mean: 47.07 Å2
Baniso -1Baniso -2Baniso -3
1--8.6907 Å20 Å2-6.0379 Å2
2--1.9039 Å20 Å2
3---6.7868 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 2.4→40.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4647 0 96 93 4836
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014856HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.146578HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1688SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes122HARMONIC2
X-RAY DIFFRACTIONt_gen_planes692HARMONIC5
X-RAY DIFFRACTIONt_it4856HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.34
X-RAY DIFFRACTIONt_other_torsion18.82
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion632SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5553SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.49 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2902 79 3.07 %
Rwork0.2289 2493 -
all0.2307 2572 -
obs--96.54 %

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