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- PDB-4fye: Crystal structure of a Legionella phosphoinositide phosphatase, SidF -

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Basic information

Entry
Database: PDB / ID: 4fye
TitleCrystal structure of a Legionella phosphoinositide phosphatase, SidF
ComponentsSidF, inhibitor of growth family, member 3
KeywordsHYDROLASE / mixed alpha-beta / phosphatase / phosphoinositides / membrane
Function / homology: / Phosphoinositide phosphatase / phosphatidylinositol phosphate phosphatase activity / membrane / PHOSPHATE ION / SidF, inhibitor of growth family, member 3
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.413 Å
AuthorsHsu, F.S. / Zhu, W. / Brennan, L. / Tao, L. / Luo, Z.Q. / Mao, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural basis for substrate recognition by a unique Legionella phosphoinositide phosphatase.
Authors: Hsu, F. / Zhu, W. / Brennan, L. / Tao, L. / Luo, Z.Q. / Mao, Y.
History
DepositionJul 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: SidF, inhibitor of growth family, member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2862
Polymers86,1911
Non-polymers951
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.176, 115.959, 124.224
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SidF, inhibitor of growth family, member 3


Mass: 86191.359 Da / Num. of mol.: 1 / Fragment: N-terminal phosphatase domain of SidF / Mutation: C645S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2584, sidF / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q5ZSD5, phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris-HCl pH8.0, 10% PEG3350, and 10% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 1, 2012 / Details: Mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.4→84.767 Å / Num. obs: 40455 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 14.8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 27.3
Reflection shellResolution: 2.4→2.49 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.413→84.767 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 18.348 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.322 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25617 2018 5 %RANDOM
Rwork0.21 ---
obs0.2123 38312 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.922 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å20 Å20 Å2
2---4.69 Å20 Å2
3---2.85 Å2
Refinement stepCycle: LAST / Resolution: 2.413→84.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5771 0 5 38 5814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.025885
X-RAY DIFFRACTIONr_angle_refined_deg2.0671.9467931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7945725
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.85325.475305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.502151087
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5831530
X-RAY DIFFRACTIONr_chiral_restr0.1590.2852
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214484
LS refinement shellResolution: 2.413→2.475 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 115 -
Rwork0.332 2238 -
obs--83.89 %
Refinement TLS params.Method: refined / Origin x: -1.8238 Å / Origin y: 45.7536 Å / Origin z: 22.3393 Å
111213212223313233
T0.0865 Å2-0.0449 Å20.0416 Å2-0.0375 Å2-0.0221 Å2--0.0838 Å2
L1.1304 °2-0.7913 °2-0.3792 °2-2.5264 °21.023 °2--1.3033 °2
S0.181 Å °-0.1396 Å °0.2591 Å °-0.1119 Å °-0.0045 Å °-0.1311 Å °-0.1483 Å °-0.0125 Å °-0.1765 Å °

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