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- PDB-2r0b: Crystal structure of human tyrosine phosphatase-like serine/threo... -

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Basic information

Entry
Database: PDB / ID: 2r0b
TitleCrystal structure of human tyrosine phosphatase-like serine/threonine/tyrosine-interacting protein
ComponentsSerine/threonine/tyrosine-interacting protein
KeywordsHYDROLASE / STRUCTURAL GENOMICS / PHOSPHATASE / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / Protein phosphatase
Function / homology
Function and homology information


negative regulation of SCF-dependent proteasomal ubiquitin-dependent catabolic process / pseudophosphatase activity / F-box domain binding / regulation of ERK1 and ERK2 cascade / negative regulation of protein binding / nucleoplasm / nucleus / cytosol / 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 domain / 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 domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Serine/threonine/tyrosine-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsBonanno, J.B. / Freeman, J. / Bain, K.T. / Iizuka, M. / Romero, R. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: J.Struct.Funct.Genom. / Year: 2007
Title: Structural genomics of protein phosphatases.
Authors: Almo, S.C. / Bonanno, J.B. / Sauder, J.M. / Emtage, S. / Dilorenzo, T.P. / Malashkevich, V. / Wasserman, S.R. / Swaminathan, S. / Eswaramoorthy, S. / Agarwal, R. / Kumaran, D. / Madegowda, M. ...Authors: Almo, S.C. / Bonanno, J.B. / Sauder, J.M. / Emtage, S. / Dilorenzo, T.P. / Malashkevich, V. / Wasserman, S.R. / Swaminathan, S. / Eswaramoorthy, S. / Agarwal, R. / Kumaran, D. / Madegowda, M. / Ragumani, S. / Patskovsky, Y. / Alvarado, J. / Ramagopal, U.A. / Faber-Barata, J. / Chance, M.R. / Sali, A. / Fiser, A. / Zhang, Z.Y. / Lawrence, D.S. / Burley, S.K.
History
DepositionAug 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300 BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. AUTHORS STATE THAT THE MONOMERIC ASSEMBLY SHOWN IN REMARK 350 IS PROBABLE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine/tyrosine-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9844
Polymers17,7001
Non-polymers2843
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.932, 53.358, 60.479
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsprobable monomer

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Components

#1: Protein Serine/threonine/tyrosine-interacting protein / Protein tyrosine phosphatase-like protein


Mass: 17699.650 Da / Num. of mol.: 1 / Fragment: Residues 26-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STYX / Plasmid: Modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8WUJ0
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6.5
Details: 100mM Bis-Tris pH 6.5, 1.8M Ammonium sulfate, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 17, 2007
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 1.6→40.011 Å / Num. all: 21898 / Num. obs: 21898 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.132 / Rsym value: 0.132 / Net I/σ(I): 8.6
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 3.9 / Num. unique all: 3120 / Rsym value: 0.343 / % possible all: 99.3

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.901 / SU B: 2.255 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.127 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1117 5.1 %RANDOM
Rwork0.26 ---
obs0.262 21839 99.63 %-
all-21839 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.565 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2--0.27 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1222 0 16 114 1352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221278
X-RAY DIFFRACTIONr_angle_refined_deg1.3951.9631726
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.435156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06923.38762
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9415224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.956159
X-RAY DIFFRACTIONr_chiral_restr0.10.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02969
X-RAY DIFFRACTIONr_nbd_refined0.2070.2615
X-RAY DIFFRACTIONr_nbtor_refined0.3160.2876
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.286
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0970.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.213
X-RAY DIFFRACTIONr_mcbond_it0.8871.5796
X-RAY DIFFRACTIONr_mcangle_it1.22221229
X-RAY DIFFRACTIONr_scbond_it2.1993555
X-RAY DIFFRACTIONr_scangle_it3.0014.5494
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 82 -
Rwork0.226 1480 -
all-1562 -
obs-1480 99.05 %

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