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- PDB-3f4a: Structure of Ygr203w, a yeast protein tyrosine phosphatase of the... -

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Basic information

Entry
Database: PDB / ID: 3f4a
TitleStructure of Ygr203w, a yeast protein tyrosine phosphatase of the Rhodanese family
ComponentsUncharacterized protein YGR203W
KeywordsHYDROLASE / protein phosphatase / rhodanese-like family / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


thiosulfate sulfurtransferase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / phosphatase activity / dephosphorylation / protein tyrosine phosphatase activity / nucleus / cytoplasm
Similarity search - Function
Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
AMMONIUM ION / CDC25-like phosphatase YCH1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsSinger, A.U. / Xu, X. / Cui, H. / Osipiuk, J. / Joachimiak, A. / Edwards, A.M. / Yakunin, A.F. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of Ygr203w, a yeast protein tyrosine phosphatase of the Rhodanese family
Authors: Proudfoot, M. / Brown, G. / Singer, A.U. / Xu, X. / Cui, H. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. / Yakunin, A.F.
History
DepositionOct 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.name / _software.version
Revision 1.3Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein YGR203W
B: Uncharacterized protein YGR203W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,79512
Polymers39,9732
Non-polymers82210
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-121 kcal/mol
Surface area14860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.382, 72.025, 53.514
Angle α, β, γ (deg.)90.00, 103.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Uncharacterized protein YGR203W


Mass: 19986.533 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: protein was digested with limiting amounts of trypsin
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: G7731, YGR203W / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD(DE3)
References: UniProt: P42937, protein-serine/threonine phosphatase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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

Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris 8,5, 1.5 M LiSO4 plus 0.015 mg/ml trypsin. Cryoprotected with N-paratone oil, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 27, 2008 / Details: Mirrors
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 27702 / Num. obs: 27354 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 25.682
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 2.6 / % possible all: 89.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXCDphasing
SHELXEmodel building
REFMAC5.2.0019refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD
Starting model: none

Resolution: 1.8→36.01 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.343 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21064 1281 5 %RANDOM
Rwork0.16575 ---
obs0.16808 24128 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.415 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→36.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2462 0 42 312 2816
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212560
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.9623484
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3725312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04622.093129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36515445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0721530
X-RAY DIFFRACTIONr_chiral_restr0.1150.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021980
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.21218
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21703
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2272
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2790.2112
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2360.242
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2361.51546
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53922401
X-RAY DIFFRACTIONr_scbond_it2.86331194
X-RAY DIFFRACTIONr_scangle_it3.8994.51078
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 91 -
Rwork0.188 1732 -
obs--97.12 %
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)
12.4872-1.0185-0.63231.35950.22843.51050.01020.1726-0.13490.0215-0.12940.1034-0.0827-0.19680.1192-0.08660.0041-0.0024-0.0891-0.0084-0.05217.696255.17543.9107
21.49920.63860.23651.57690.52351.45390.0775-0.10590.08250.1358-0.10640.0407-0.0412-0.09870.0289-0.0246-0.05460.0083-0.0626-0.0112-0.068511.378736.329321.2831
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 148
2X-RAY DIFFRACTION2B5 - 148

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