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- PDB-5jpf: Serine/Threonine phosphatase Z1 (Candida albicans) binds to inhib... -

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Basic information

Entry
Database: PDB / ID: 5jpf
TitleSerine/Threonine phosphatase Z1 (Candida albicans) binds to inhibitor microcystin-LR
Components
  • Microcystin-LR
  • Serine/threonine-protein phosphatase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / yeast-specific serine/threonine phosphatase / microcystin-LR / HYDROLASE-HYDROLASE INHIBITOR complex
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
Microcystin LR / MALONATE ION / : / : / Serine/threonine-protein phosphatase
Similarity search - Component
Biological speciesCandida albicans (yeast)
Microcystis aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.39929733252 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: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_oper_list / pdbx_validate_polymer_linkage
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 ...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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _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_conn_type.id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_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
M: Microcystin-LR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4847
Polymers37,0682
Non-polymers4165
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-7 kcal/mol
Surface area12010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.665, 50.665, 201.054
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"

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Components

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


Mass: 36053.473 Da / Num. of mol.: 1 / Fragment: UNP residues 171-484
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: Protein/peptide Microcystin-LR


Type: Oligopeptide / Class: Toxin / Mass: 1014.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Microcystis aeruginosa (bacteria) / References: NOR: NOR00109, Microcystin LR
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.19 Å3/Da / Density % sol: 38.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.1 / Details: 0.06 M citric acid, pH 4.1, 16% w/v PEG3350

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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: Dec 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 12331 / % possible obs: 98.5 % / Redundancy: 6.1 % / Biso Wilson estimate: 31.3055033723 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.8
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.442.70.1975100.93284.2
2.44-2.492.80.1965281.0689.8
2.49-2.533.40.1816130.99596.5
2.53-2.593.90.1835910.9699.8
2.59-2.644.80.1576141.014100
2.64-2.76.20.1665931.055100
2.7-2.776.90.1516201.02100
2.77-2.8570.1336241.041100
2.85-2.936.80.1146061.074100
2.93-3.027.10.0956121.148100
3.02-3.136.90.0866201.192100
3.13-3.2670.0796121.32100
3.26-3.416.90.0716341.494100
3.41-3.5870.0646071.59499.8
3.58-3.816.70.0686472.746100
3.81-4.16.90.0576072.151100
4.1-4.526.70.056482.58100
4.52-5.1770.0456521.789100
5.17-6.516.90.056621.462100
6.51-506.40.0437311.9899.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.6 Å43.88 Å
Translation6.6 Å43.88 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JPE

5jpe


Resolution: 2.39929733252→43.8771770827 Å / SU ML: 0.251334000047 / Cross valid method: FREE R-VALUE / σ(F): 1.34237012989 / Phase error: 22.1299322925
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.234480797525 637 5.18602947163 %
Rwork0.178764472004 11646 -
obs0.181591154876 12283 98.5241036336 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.8085424173 Å2
Refinement stepCycle: LAST / Resolution: 2.39929733252→43.8771770827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2385 0 23 50 2458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003475379636682469
X-RAY DIFFRACTIONf_angle_d0.5672314091743331
X-RAY DIFFRACTIONf_chiral_restr0.0411586764162370
X-RAY DIFFRACTIONf_plane_restr0.00302714063993431
X-RAY DIFFRACTIONf_dihedral_angle_d10.99929242531425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3993-2.58450.3185959562791060.20574463392129X-RAY DIFFRACTION92.5849212925
2.5845-2.84460.2785925363031330.2197325534482317X-RAY DIFFRACTION100
2.8446-3.25610.2704851226971380.1956499415312306X-RAY DIFFRACTION100
3.2561-4.10180.1952047393481270.1678744374312359X-RAY DIFFRACTION100
4.1018-43.88450.2093995493541330.1584559633352535X-RAY DIFFRACTION99.925093633

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