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- PDB-4jza: Crystal structure of a Legionella phosphoinositide phosphatase: i... -

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Basic information

Entry
Database: PDB / ID: 4jza
TitleCrystal structure of a Legionella phosphoinositide phosphatase: insights into lipid metabolism in pathogen host interaction
ComponentsUncharacterized protein
KeywordsHYDROLASE / alpha beta fold / phosphatase
Function / homology
Function and homology information


Peroxidase; domain 1 - #60 / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1720 / Phosphoinositide phosphatase insertion domain / Phosphoinositide phosphatase, C-terminal / Phosphoinositide phosphatase insertion domain / Phosphoinositide phosphatase C-terminal domain / Peroxidase; domain 1 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesLegionella longbeachae NSW150 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.584 Å
AuthorsToulabi, L. / Wu, X. / Cheng, Y. / Mao, Y.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Identification and structural characterization of a legionella phosphoinositide phosphatase.
Authors: Toulabi, L. / Wu, X. / Cheng, Y. / Mao, Y.
History
DepositionApr 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Sep 11, 2013Group: Database references
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)190,1002
Polymers190,1002
Non-polymers00
Water2,900161
1
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)95,0501
Polymers95,0501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)95,0501
Polymers95,0501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-12 kcal/mol
Surface area70770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.280, 119.653, 133.533
Angle α, β, γ (deg.)90.00, 101.33, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.913794, 0.032049, 0.404912), (0.033455, -0.999434, 0.003604), (0.404799, 0.010253, -0.914348)-34.47376, 30.23039, 159.70755

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Components

#1: Protein Uncharacterized protein


Mass: 95049.992 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Legionella longbeachae NSW150 (bacteria) / Strain: NSW150
References: UniProt: D3HMN4, phosphatidylinositol-3-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.7 Å3/Da / Density % sol: 66.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES (pH 7.0), 0.1M succinic acid, and 6.5% (wt/vol) PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2012 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.58→130.93 Å / Num. all: 167313 / Num. obs: 164803 / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.099 / Net I/σ(I): 10.96

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.584→49.44 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 19.411 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.372 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23695 4205 5 %RANDOM
Rwork0.1958 ---
obs0.19788 79616 97.12 %-
all-80827 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.829 Å2
Baniso -1Baniso -2Baniso -3
1-5.47 Å2-0 Å2-0.47 Å2
2---1.39 Å2-0 Å2
3----3.69 Å2
Refinement stepCycle: LAST / Resolution: 2.584→49.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13182 0 0 161 13343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01913521
X-RAY DIFFRACTIONr_bond_other_d0.0050.0212809
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.9718333
X-RAY DIFFRACTIONr_angle_other_deg1.128329552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.09151633
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.19724.215643
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.493152339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1211583
X-RAY DIFFRACTIONr_chiral_restr0.0890.22026
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02115158
X-RAY DIFFRACTIONr_gen_planes_other0.0140.023093
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_it3.7154.3896538
X-RAY DIFFRACTIONr_mcbond_other3.7084.3896537
X-RAY DIFFRACTIONr_mcangle_it5.8486.5738169
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.2414.7676983
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.584→2.651 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 240 -
Rwork0.308 4642 -
obs--77.02 %
Refinement TLS params.

S13: 0.0173 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.02480.0127-0.0340.248-0.00290.5220.0666-0.0020.0485-0.03480.0266-0.00460.0405-0.03190.1729-0.00530.02030.09730.0030.049846.665933.1987105.3961
20.0285-0.047-0.04810.40360.07290.29540.04810.00170.0056-0.014-0.02720.07040.0133-0.03410.145-0.0204-0.02170.11830.01230.086552.2703-0.926882.585
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 824
2X-RAY DIFFRACTION2B2 - 824

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