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- PDB-5jpe: Yeast-specific serine/threonine protein phosphatase (PPZ1) of Can... -

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Basic information

Entry
Database: PDB / ID: 5jpe
TitleYeast-specific serine/threonine protein phosphatase (PPZ1) of Candida albicans
ComponentsSerine/threonine-protein phosphatase
KeywordsHYDROLASE / Yeast serine/threonine protein phosphatase
Function / homology
Function and homology information


myosin phosphatase activity / protein-serine/threonine phosphatase / metal ion binding / cytoplasm
Similarity search - Function
Phosphoprotein phosphatase PPZ/Ppq1 / Serine-threonine protein phosphatase, N-terminal / Serine-threonine protein phosphatase N-terminal domain / 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 ...Phosphoprotein phosphatase PPZ/Ppq1 / Serine-threonine protein phosphatase, N-terminal / Serine-threonine protein phosphatase N-terminal domain / 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 / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Serine/threonine-protein phosphatase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.611 Å
AuthorsChoy, M.S. / Chen, E.H. / Peti, W. / Page, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098482 United States
CitationJournal: Mbio / Year: 2016
Title: Molecular Insights into the Fungus-Specific Serine/Threonine Protein Phosphatase Z1 in Candida albicans.
Authors: Chen, E. / Choy, M.S. / Petrenyi, K. / Konya, Z. / Erdodi, F. / Dombradi, V. / Peti, W. / Page, R.
History
DepositionMay 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase
B: Serine/threonine-protein phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1125
Polymers70,6412
Non-polymers4703
Water3,963220
1
A: Serine/threonine-protein phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5102
Polymers35,3211
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6023
Polymers35,3211
Non-polymers2812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.975, 183.727, 69.038
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-669-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: GLN / End label comp-ID: GLN

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1HISHISchain AAA169 - 4782 - 311
2ASPASPchain BBB172 - 4785 - 311

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Components

#1: Protein Serine/threonine-protein phosphatase / Serine/threonine phosphatase Z1


Mass: 35320.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: CAWG_01946 / Production host: Escherichia coli (E. coli)
References: UniProt: C4YM68, protein-serine/threonine phosphatase
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 220 / 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: 3.25 Å3/Da / Density % sol: 62.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.8 M ammonium citrate tribasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.61→50 Å / Num. obs: 28438 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 36.73 Å2 / Rmerge(I) obs: 0.133 / Χ2: 1.131 / Net I/av σ(I): 14.09 / Net I/σ(I): 5.8 / Num. measured all: 158500
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.61-2.665.60.8451100
2.66-2.75.60.6711100
2.7-2.765.60.6731100
2.76-2.815.60.5741100
2.81-2.875.60.4871100
2.87-2.945.60.3831100
2.94-3.015.70.3031100
3.01-3.095.60.2511100
3.09-3.195.60.2041100
3.19-3.295.70.1711100
3.29-3.415.60.1551100
3.41-3.545.60.1321100
3.54-3.75.60.1291100
3.7-3.95.60.121100
3.9-4.145.50.101199.9
4.14-4.465.50.0771100
4.46-4.915.60.073199.9
4.91-5.625.60.0771100
5.62-7.085.50.0871100
7.08-505.20.042199.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.61 Å36.24 Å
Translation2.61 Å36.24 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4MOV

4mov


Resolution: 2.611→36.244 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.4
RfactorNum. reflection% reflection
Rfree0.2219 1390 4.91 %
Rwork0.1935 --
obs0.1949 28311 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.82 Å2 / Biso mean: 32.9482 Å2 / Biso min: 12.41 Å2
Refinement stepCycle: final / Resolution: 2.611→36.244 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4922 0 32 220 5174
Biso mean--29.98 30.86 -
Num. residues----617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025064
X-RAY DIFFRACTIONf_angle_d0.7196860
X-RAY DIFFRACTIONf_chiral_restr0.028760
X-RAY DIFFRACTIONf_plane_restr0.003883
X-RAY DIFFRACTIONf_dihedral_angle_d13.4611855
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2891X-RAY DIFFRACTION6.508TORSIONAL
12B2891X-RAY DIFFRACTION6.508TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6107-2.7040.32591310.25982636276799
2.704-2.81220.31841230.252726602783100
2.8122-2.94020.28881690.239726592828100
2.9402-3.09510.28091500.235426552805100
3.0951-3.28890.2611400.224626912831100
3.2889-3.54260.22211190.204326872806100
3.5426-3.89880.26021330.187827082841100
3.8988-4.4620.18621230.16852665278898
4.462-5.61830.1791350.15672719285499
5.6183-36.24720.14631670.160128413008100

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