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- PDB-5nny: Crystal structure of the phosphatase domain from the Legionella e... -

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Basic information

Entry
Database: PDB / ID: 5nny
TitleCrystal structure of the phosphatase domain from the Legionella effector WipB
ComponentsWipB
KeywordsHYDROLASE / Legionella effector / Serine/Threonine phosphatase / phosphoesterase fold
Function / homologyDomain of unknown function DUF5617 / Domain of unknown function (DUF5617) / WipB
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPinotsis, N. / Waksman, G. / Prevost, M.S.
Funding support Belgium, 1items
OrganizationGrant numberCountry
European Research Council321630 Belgium
Citation
Journal: Sci Rep / Year: 2017
Title: The Legionella effector WipB is a translocated Ser/Thr phosphatase that targets the host lysosomal nutrient sensing machinery.
Authors: Prevost, M.S. / Pinotsis, N. / Dumoux, M. / Hayward, R.D. / Waksman, G.
#1: Journal: To Be Published
Title: Structure of WipA reveals a novel tyrosine protein phosphatase effector from Legionella pneumophila
Authors: Pinotsis, N. / Waksman, G. / Prevost, M.S.
History
DepositionApr 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WipB
B: WipB


Theoretical massNumber of molelcules
Total (without water)72,6752
Polymers72,6752
Non-polymers00
Water8,719484
1
A: WipB


Theoretical massNumber of molelcules
Total (without water)36,3371
Polymers36,3371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: WipB


Theoretical massNumber of molelcules
Total (without water)36,3371
Polymers36,3371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.400, 79.100, 79.700
Angle α, β, γ (deg.)90.00, 98.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein WipB


Mass: 36337.312 Da / Num. of mol.: 2 / Fragment: Phosphatase domain, UNP Residues 25-344
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: wipB / Production host: Escherichia coli (E. coli) / References: UniProt: Q5GA15
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5 / Details: 0.23 M ammonium citrate dibasic and 22% PEG3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.7→48.832 Å / Num. obs: 66193 / % possible obs: 99.3 % / Redundancy: 3.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.116 / Net I/σ(I): 8.73
Reflection shellResolution: 1.7→1.74 Å / Mean I/σ(I) obs: 1.21 / Num. unique obs: 4732 / CC1/2: 0.48 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N6X

5n6x


Resolution: 1.7→48.832 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2173 3204 4.84 %
Rwork0.1874 --
obs0.1888 66191 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→48.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4982 0 0 484 5466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075182
X-RAY DIFFRACTIONf_angle_d0.8487016
X-RAY DIFFRACTIONf_dihedral_angle_d20.4133104
X-RAY DIFFRACTIONf_chiral_restr0.053781
X-RAY DIFFRACTIONf_plane_restr0.005907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72540.34711360.32592582X-RAY DIFFRACTION95
1.7254-1.75230.34581440.31512737X-RAY DIFFRACTION100
1.7523-1.78110.28411430.30342718X-RAY DIFFRACTION100
1.7811-1.81180.31731450.28062755X-RAY DIFFRACTION100
1.8118-1.84470.31181420.28522709X-RAY DIFFRACTION99
1.8447-1.88020.31181430.27722704X-RAY DIFFRACTION99
1.8802-1.91860.3031290.25862762X-RAY DIFFRACTION99
1.9186-1.96030.28981360.23682710X-RAY DIFFRACTION99
1.9603-2.00590.26981340.22232745X-RAY DIFFRACTION100
2.0059-2.05610.24831390.20142751X-RAY DIFFRACTION100
2.0561-2.11170.22241390.19452720X-RAY DIFFRACTION100
2.1117-2.17380.25471390.18642790X-RAY DIFFRACTION100
2.1738-2.2440.23711370.1722742X-RAY DIFFRACTION100
2.244-2.32420.23041380.172718X-RAY DIFFRACTION99
2.3242-2.41720.23741410.17792742X-RAY DIFFRACTION100
2.4172-2.52720.22621360.17792759X-RAY DIFFRACTION100
2.5272-2.66050.23651430.17742761X-RAY DIFFRACTION100
2.6605-2.82720.20391400.17392752X-RAY DIFFRACTION100
2.8272-3.04540.21841360.17482734X-RAY DIFFRACTION99
3.0454-3.35180.15221430.17292776X-RAY DIFFRACTION100
3.3518-3.83670.16271390.15712752X-RAY DIFFRACTION99
3.8367-4.83310.19811410.15052747X-RAY DIFFRACTION99
4.8331-48.85170.18561410.18882821X-RAY DIFFRACTION99
Refinement TLS params.

S33: -0 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2388-0.14980.01630.21090.34710.4840.0071-0.0065-0.00850.02260.00850.0174-0.01780.02520.1154-0.0040.00050.0908-0.00250.10515.1593-14.15027.8092
20.43110.10570.32790.15650.01380.11940.0120.01250.07840.036-0.01570.0464-0.00090.06320.1374-0.0111-0.00060.1507-0.00180.116312.03376.034222.7644
30.24070.02090.13310.2467-0.10540.4190.0097-0.01110.019-0.0117-0.03220.0028-0.03860.03960.0866-0.00260.010.1047-0.01330.121815.5392-8.0334-17.3912
40.0732-0.1584-0.0790.0640.30750.26210.06630.05020.0563-0.0143-0.0702-0.0251-0.0763-0.09420.16510.01770.00140.15320.0070.1796-3.85811.6741-26.7481
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 24:213))
2X-RAY DIFFRACTION2chain 'A' and ((resseq 214:331))
3X-RAY DIFFRACTION3chain 'B' and ((resseq 25:225))
4X-RAY DIFFRACTION4chain 'B' and ((resseq 226:344))

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