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- PDB-3s3h: Crystal structure of the catalytic domain of PTP10D from Drosophi... -

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Basic information

Entry
Database: PDB / ID: 3s3h
TitleCrystal structure of the catalytic domain of PTP10D from Drosophila melanogaster with a phosphopeptide substrate GP4
Components
  • Tyrosine-protein phosphatase 10D
  • phosphopeptide GP4
KeywordsHYDROLASE / Differentiation / Neurogenesis / Signal transduction / developmental Protein / Protein Phosphatase / Protein Tyrosine Phosphatase
Function / homology
Function and homology information


branching involved in open tracheal system development / open tracheal system development / negative regulation of fibroblast growth factor receptor signaling pathway / Neutrophil degranulation / transmembrane receptor protein tyrosine phosphatase activity / motor neuron axon guidance / negative regulation of epidermal growth factor receptor signaling pathway / negative regulation of vascular endothelial growth factor receptor signaling pathway / long-term memory / protein dephosphorylation ...branching involved in open tracheal system development / open tracheal system development / negative regulation of fibroblast growth factor receptor signaling pathway / Neutrophil degranulation / transmembrane receptor protein tyrosine phosphatase activity / motor neuron axon guidance / negative regulation of epidermal growth factor receptor signaling pathway / negative regulation of vascular endothelial growth factor receptor signaling pathway / long-term memory / protein dephosphorylation / protein-tyrosine-phosphatase / central nervous system development / protein tyrosine phosphatase activity / axon guidance / apical part of cell / axon / 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 / Protein tyrosine phosphatase, catalytic domain motif ...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
1-BUTANOL / 1,4-BUTANEDIOL / Tyrosine-protein phosphatase 10D
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMadan, L.L. / Gopal, B.
CitationJournal: Biochemistry / Year: 2011
Title: Conformational basis for substrate recruitment in protein tyrosine phosphatase 10D
Authors: Madan, L.L. / Gopal, B.
History
DepositionMay 18, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Nov 1, 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_ncs_dom_lim / 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 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

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase 10D
B: Tyrosine-protein phosphatase 10D
C: phosphopeptide GP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4805
Polymers73,3163
Non-polymers1642
Water1,47782
1
A: Tyrosine-protein phosphatase 10D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1103
Polymers35,9461
Non-polymers1642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosine-protein phosphatase 10D
C: phosphopeptide GP4


Theoretical massNumber of molelcules
Total (without water)37,3702
Polymers37,3702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-7 kcal/mol
Surface area12570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.700, 102.700, 173.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 4 / Auth seq-ID: 21 - 305 / Label seq-ID: 21 - 305

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

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Components

#1: Protein Tyrosine-protein phosphatase 10D / Receptor-linked protein-tyrosine phosphatase 10D / DPTP10D


Mass: 35945.633 Da / Num. of mol.: 2 / Fragment: UNP residues 1250-1533
Source method: isolated from a genetically manipulated source
Details: Central nervous system / Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG1817, Ptp10D / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P35992, protein-tyrosine-phosphatase
#2: Protein/peptide phosphopeptide GP4


Mass: 1424.491 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide
#3: Chemical ChemComp-1BO / 1-BUTANOL / BUTAN-1-OL / 1-Butanol


Mass: 74.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O
#4: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL / 1,4-Butanediol


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 3.6 Å3/Da / Density % sol: 65.8 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 15% PEG4000, 120mM Citrate, 10% iso-propanol, 10% n-Butanol, 10% 1,4-Butanediol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 30, 2010 / Details: BENT COLLIMATING MIRROR AND TOROID
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→45 Å / Num. obs: 26708 / % possible obs: 100 % / Observed criterion σ(I): -5 / Redundancy: 5.3 % / Biso Wilson estimate: 54.12 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 10.6
Reflection shellResolution: 2.8→2.95 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3S3E

3s3e


Resolution: 2.8→44.47 Å / Cor.coef. Fo:Fc: 0.859 / Cor.coef. Fo:Fc free: 0.815 / SU B: 28.434 / SU ML: 0.266 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1343 5 %RANDOM
Rwork0.25 ---
obs0.252 25293 99.9 %-
all-25293 --
Solvent computationSolvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 49.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.05 Å20 Å2
2--0.11 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.8→44.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4691 0 11 82 4784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224841
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.9286565
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0635570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21222.731260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.97815777
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4521549
X-RAY DIFFRACTIONr_chiral_restr0.1010.2681
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213812
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCSNumber: 2261 / Type: medium positional / Rms dev position: 0.63 Å / Weight position: 0.5
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 89 -
Rwork0.308 1827 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6821-0.4010.01291.3151-0.01843.22810.0179-0.1041-0.01410.0088-0.0016-0.02830.09850.2896-0.01630.0110.0047-0.02550.03430.00750.087334.894713.48866.2224
21.47470.1175-0.56991.42340.06472.89530.0012-0.2282-0.0270.21870.0651-0.00850.04790.0771-0.06640.04830.0142-0.01250.0638-0.01860.08619.511933.403531.2858
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 305
2X-RAY DIFFRACTION2B21 - 305

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