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

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Basic information

Entry
Database: PDB / ID: 4fyf
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 / : / 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: 2.424 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)86,8885
Polymers86,1911
Non-polymers6974
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.835, 115.709, 125.114
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Hg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 3.02 Å3/Da / Density % sol: 59.22 %
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: CHESS / Beamline: A1 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2011 / 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: 2.42→50 Å / Num. all: 40322 / Num. obs: 39764 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 22.3
Reflection shellResolution: 2.42→2.49 Å / % possible all: 99.5

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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
Starting model: SIRAS

Resolution: 2.424→47.18 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.91 / SU B: 15.779 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.345 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26971 1988 5 %RANDOM
Rwork0.21059 ---
obs0.21354 37660 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.82 Å2
Baniso -1Baniso -2Baniso -3
1-1.81 Å20 Å20 Å2
2---3.35 Å20 Å2
3---1.54 Å2
Refinement stepCycle: LAST / Resolution: 2.424→47.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5890 0 8 69 5967
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.026018
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0291.9458114
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6815744
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.92225.397315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.066151114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6581533
X-RAY DIFFRACTIONr_chiral_restr0.1650.2871
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214597
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.424→2.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 124 -
Rwork0.296 2225 -
obs--84.59 %
Refinement TLS params.Method: refined / Origin x: -2.4762 Å / Origin y: 45.9109 Å / Origin z: 22.0993 Å
111213212223313233
T0.0534 Å2-0.0204 Å20.0454 Å2-0.0289 Å2-0.0283 Å2--0.0516 Å2
L0.9924 °2-0.6034 °2-0.3123 °2-1.9345 °20.7996 °2--1.303 °2
S0.1683 Å °-0.1154 Å °0.214 Å °-0.0393 Å °-0.0742 Å °-0.0654 Å °-0.16 Å °-0.0642 Å °-0.094 Å °

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