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- PDB-2j16: Apo & Sulphate bound forms of SDP-1 -

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Basic information

Entry
Database: PDB / ID: 2j16
TitleApo & Sulphate bound forms of SDP-1
Components(TYROSINE-PROTEIN PHOSPHATASE YIL113W) x 2
KeywordsHYDROLASE / PROTEIN PHOSPHATASE / HYPOTHETICAL PROTEIN
Function / homology
Function and homology information


cell integrity MAPK cascade / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / negative regulation of MAPK cascade / protein-tyrosine-phosphatase / signal transduction / nucleus / cytoplasm
Similarity search - Function
Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. ...Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Dual-specificity protein phosphatase SDP1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBriggs, D.C. / McDonald, N.Q.
CitationJournal: Nature / Year: 2007
Title: Redox-mediated substrate recognition by Sdp1 defines a new group of tyrosine phosphatases.
Authors: Fox, G.C. / Shafiq, M. / Briggs, D.C. / Knowles, P.P. / Collister, M. / Didmon, M.J. / Makrantoni, V. / Dickinson, R.J. / Hanrahan, S. / Totty, N. / Stark, M.J. / Keyse, S.M. / McDonald, N.Q.
History
DepositionAug 9, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5May 1, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TYROSINE-PROTEIN PHOSPHATASE YIL113W
B: TYROSINE-PROTEIN PHOSPHATASE YIL113W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0856
Polymers41,7722
Non-polymers3124
Water73941
1
A: TYROSINE-PROTEIN PHOSPHATASE YIL113W


Theoretical massNumber of molelcules
Total (without water)20,9021
Polymers20,9021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: TYROSINE-PROTEIN PHOSPHATASE YIL113W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1825
Polymers20,8701
Non-polymers3124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)77.342, 77.342, 152.885
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.749, 0.6625, 0.004), (0.6616, 0.7482, -0.0496), (-0.0358, -0.0345, -0.9988)
Vector: 16.5778, -5.1841, 47.3358)

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Components

#1: Protein TYROSINE-PROTEIN PHOSPHATASE YIL113W / SDP-1


Mass: 20902.004 Da / Num. of mol.: 1 / Fragment: RESIDUES 17-198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / AB972 / Plasmid: PET14B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): FB810 / Variant (production host): PLYSS / References: UniProt: P40479, protein-tyrosine-phosphatase
#2: Protein TYROSINE-PROTEIN PHOSPHATASE YIL113W / SDP-1


Mass: 20870.004 Da / Num. of mol.: 1 / Fragment: RESIDUES 17-198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / AB972 / Plasmid: PET14B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): FB810 / Variant (production host): PLYSS / References: UniProt: P40479, protein-tyrosine-phosphatase
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.65 Å3/Da / Density % sol: 66.01 %
Crystal growMethod: vapor diffusion, sitting drop
Details: 1.5M MGSO4, 0.1M HEPES, PH 7.5 7MG/ML PROTEIN 1:1 SITTING DROP VAPOUR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 1, 2000 / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 13396 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Rmerge(I) obs: 0.06
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.37 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ENSEMBLE MODEL

Resolution: 2.7→19.77 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.903 / SU B: 10.719 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.498 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS AND SIDECHAIN ATOMS WERE OMMITTED.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 652 4.9 %RANDOM
Rwork0.23 ---
obs0.232 12583 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2179 0 16 41 2236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222247
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.9813069
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6355273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.41124.2789
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.24915374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.589157
X-RAY DIFFRACTIONr_chiral_restr0.0830.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021647
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.21002
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21505
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.270
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5711.51429
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.03722251
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.8693937
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.4254.5818
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: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.311 47
Rwork0.302 897

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