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- PDB-4fyg: Structural basis for substrate recognition by a novel Legionella ... -

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Basic information

Entry
Database: PDB / ID: 4fyg
TitleStructural basis for substrate recognition by a novel Legionella phosphoinositide phosphatase
ComponentsSidF, inhibitor of growth family, member 3
KeywordsHYDROLASE / mixed alpha-beta / phosphoinositide phosphatase / phosphoinositides / membrane
Function / homology: / Phosphoinositide phosphatase / phosphatidylinositol phosphate phosphatase activity / membrane / Chem-3PT / SidF, inhibitor of growth family, member 3
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.822 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 1.2Sep 13, 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_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)86,8262
Polymers86,1911
Non-polymers6341
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.230, 114.833, 124.366
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 (UNP Residues 1-760)
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-3PT / (2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6S)-2,3,6-trihydroxy-4,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dibutanoate


Mass: 634.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H33O19P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.95 Å3/Da / Density % sol: 58.31 %
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 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9789 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 4, 2012 / Details: mirrors
RadiationMonochromator: Single crystal bender / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.82→50 Å / Num. all: 301119 / Num. obs: 24387 / % possible obs: 96.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12.3 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 28.6
Reflection shellResolution: 2.82→2.9 Å / % possible all: 78.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 4FYF

4fyf


Resolution: 2.822→36.58 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.91 / SU B: 30.281 / SU ML: 0.272 / Cross valid method: THROUGHOUT / ESU R Free: 0.375 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2522 1246 5.1 %RANDOM
Rwork0.17907 ---
obs0.18279 22955 95.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.396 Å2
Baniso -1Baniso -2Baniso -3
1-4.92 Å20 Å20 Å2
2---4.77 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.822→36.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5923 0 39 6 5968
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.026067
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.9538179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4615742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.88925.382314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.045151116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3121533
X-RAY DIFFRACTIONr_chiral_restr0.1160.2879
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214609
LS refinement shellResolution: 2.822→2.895 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 74 -
Rwork0.274 1164 -
obs--71.73 %
Refinement TLS params.Method: refined / Origin x: -2.5584 Å / Origin y: 45.7343 Å / Origin z: 21.9739 Å
111213212223313233
T0.0833 Å2-0.072 Å20.0428 Å2-0.1086 Å2-0.0476 Å2--0.0429 Å2
L1.1072 °2-0.5332 °2-0.4577 °2-2.6096 °20.7847 °2--1.4611 °2
S0.1657 Å °-0.2106 Å °0.1938 Å °-0.2138 Å °-0.0142 Å °-0.0664 Å °-0.1387 Å °-0.0026 Å °-0.1515 Å °

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