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- PDB-4tvv: Crystal structure of LppA from Legionella pneumophila -

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Basic information

Entry
Database: PDB / ID: 4tvv
TitleCrystal structure of LppA from Legionella pneumophila
ComponentsTyrosine phosphatase II superfamily protein
KeywordsHYDROLASE / bacterial effector protein / phytase / myo-inositol-hexakisphosphate
Function / homology
Function and homology information


phosphoprotein phosphatase activity
Similarity search - Function
Inositol hexakisphosphate / Inositol hexakisphosphate / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Tyrosine phosphatase II superfamily protein
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsWeber, S. / Stirnimann, C. / Wieser, M. / Meier, R. / Engelhardt, S. / Li, X. / Capitani, G. / Kammerer, R. / Hilbi, H.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: A Type IV Translocated Legionella Cysteine Phytase Counteracts Intracellular Growth Restriction by Phytate.
Authors: Weber, S. / Stirnimann, C.U. / Wieser, M. / Frey, D. / Meier, R. / Engelhardt, S. / Li, X. / Capitani, G. / Kammerer, R.A. / Hilbi, H.
History
DepositionJun 28, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine phosphatase II superfamily protein
B: Tyrosine phosphatase II superfamily protein
C: Tyrosine phosphatase II superfamily protein
D: Tyrosine phosphatase II superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,09119
Polymers143,9394
Non-polymers1,15115
Water26,3741464
1
A: Tyrosine phosphatase II superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2465
Polymers35,9851
Non-polymers2614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine phosphatase II superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4607
Polymers35,9851
Non-polymers4756
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tyrosine phosphatase II superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2104
Polymers35,9851
Non-polymers2253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tyrosine phosphatase II superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1753
Polymers35,9851
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.650, 55.490, 131.420
Angle α, β, γ (deg.)90.00, 99.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Tyrosine phosphatase II superfamily protein


Mass: 35984.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2819 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZRR1

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Non-polymers , 5 types, 1479 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1464 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 40 mM KH2PO4 ph 4.1, 16% PEG 8000, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 264769 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Net I/σ(I): 15.9
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.3 / % possible all: 90.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F41

3f41


Resolution: 1.4→48.259 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 16.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1686 1060 0.4 %RANDOM
Rwork0.1434 ---
obs0.1435 264665 95.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→48.259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9244 0 59 1464 10767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079694
X-RAY DIFFRACTIONf_angle_d1.13213177
X-RAY DIFFRACTIONf_dihedral_angle_d13.3813603
X-RAY DIFFRACTIONf_chiral_restr0.0641418
X-RAY DIFFRACTIONf_plane_restr0.0061683
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3999-1.46370.26921240.220830749X-RAY DIFFRACTION90
1.4637-1.54080.1821270.170531568X-RAY DIFFRACTION92
1.5408-1.63740.18971310.143832733X-RAY DIFFRACTION96
1.6374-1.76380.17421340.126333207X-RAY DIFFRACTION97
1.7638-1.94130.1681340.122933446X-RAY DIFFRACTION98
1.9413-2.22220.16281350.118433668X-RAY DIFFRACTION98
2.2222-2.79970.16471360.1333911X-RAY DIFFRACTION99
2.7997-48.28730.1611390.157734323X-RAY DIFFRACTION98

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