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- PDB-3icf: Structure of Protein serine/threonine phosphatase from Saccharomy... -

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Basic information

Entry
Database: PDB / ID: 3icf
TitleStructure of Protein serine/threonine phosphatase from Saccharomyces cerevisiae with similarity to human phosphatase PP5
ComponentsSerine/threonine-protein phosphatase T
KeywordsHYDROLASE / phosphatase / serine/threonine / saccharomyces cerevisiae / iron / metalloprotein / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Manganese / Metal-binding / Nucleus / Protein phosphatase / TPR repeat
Function / homology
Function and homology information


ESR-mediated signaling / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / protein dephosphorylation / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine/threonine protein phosphatase 5 / PPP domain / PP5, C-terminal metallophosphatase domain / PPP5 TPR repeat region / : / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 ...Serine/threonine protein phosphatase 5 / PPP domain / PP5, C-terminal metallophosphatase domain / PPP5 TPR repeat region / : / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / 4-Layer Sandwich / Tetratricopeptide-like helical domain superfamily / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Serine/threonine-protein phosphatase T
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSinger, A.U. / Xu, X. / Chang, C. / Cui, H. / Kagan, O. / Edwards, A.M. / Joachimiak, A. / Yakunin, A.F. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of Protein serine/threonine phosphatase from Saccharomyces cerevisiae with similarity to human phosphatase PP5
Authors: Singer, A.U. / Xu, X. / Chang, C. / Cui, H. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. / Yakunin, A.F.
History
DepositionJul 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 22, 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: Serine/threonine-protein phosphatase T
B: Serine/threonine-protein phosphatase T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,35012
Polymers76,7542
Non-polymers59610
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-90 kcal/mol
Surface area24140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.194, 47.194, 237.096
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A190 - 510
2111B190 - 510

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Serine/threonine-protein phosphatase T / PPT


Mass: 38376.840 Da / Num. of mol.: 2 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: G6347, PPT1, YGR123C / Plasmid: p15Tv Lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL
References: UniProt: P53043, protein-serine/threonine phosphatase

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Non-polymers , 6 types, 86 molecules

#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE AUTHOR STATES THAT THE STRUCTURE WAS SOLVED WITH LIMITING AMOUNTS OF V8 PROTEASE ADDED TO THE ...THE AUTHOR STATES THAT THE STRUCTURE WAS SOLVED WITH LIMITING AMOUNTS OF V8 PROTEASE ADDED TO THE CRYSTALLIZATION LIQUOR AS A WAY TO ENHANCE CRYSTALLIZATION. THUS THOUGH THE INITIAL PROTEIN WAS INDEED FULL-LENGTH, ONLY THE CATALYTIC DOMAIN IS OBSERVED IN THE STRUCTURE, NOT THE N-TERMINAL TPR REPEATS. WE HAVE NOT CONFIRMED THE CRYSTALLIZED FRAGMENT BY MASS SPEC, BUT BELEIVE THE N-TERMINAL 178 RESIDUES HAVE BEEN REMOVED BY THE V8 PROTEASE.

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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: 2.04 Å3/Da / Density % sol: 39.62 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes 7.5, 0.2 M NaCl, 25% PEG3350 plus 0.015 mg/ml V8 protease. Cryoprotected with Paratone-N oil, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 17, 2008 / Details: mirrors
RadiationMonochromator: SI-111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.3→40.29 Å / Num. all: 26308 / Num. obs: 25761 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 29.286
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 3.5 / % possible all: 82.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-3000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1WAO

1wao


Resolution: 2.3→40.29 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.93 / SU B: 19.778 / SU ML: 0.229 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.521 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23994 1283 5 %RANDOM
Rwork0.18993 ---
obs0.19244 24379 97.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.813 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5045 0 24 76 5145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225211
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.956998
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9695627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.1824.307267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.90115872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0511528
X-RAY DIFFRACTIONr_chiral_restr0.110.2719
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024040
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.22548
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.23497
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2243
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.10.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6031.53137
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.11725036
X-RAY DIFFRACTIONr_scbond_it2.10932116
X-RAY DIFFRACTIONr_scangle_it3.0364.51962
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2513 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.070.05
tight thermal0.170.5
LS refinement shellResolution: 2.3→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 84 -
Rwork0.284 1527 -
obs--80.23 %
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)
11.1524-0.2043-0.45451.88360.01226.4084-0.14670.0656-0.06040.00950.2182-0.06030.33110.093-0.0716-0.3297-0.08750.0415-0.1046-0.0536-0.07417.2676-9.540413.241
21.86220.2055-0.23711.37930.2896.39550.11220.15160.01840.2058-0.01940.09380.1013-0.3011-0.0928-0.07370.0590.0704-0.3564-0.0134-0.08216.6928-3.461853.3666
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A188 - 506
2X-RAY DIFFRACTION2B188 - 506

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