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- PDB-5y9o: The apo structure of Legionella pneumophila WipA -

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Basic information

Entry
Database: PDB / ID: 5y9o
TitleThe apo structure of Legionella pneumophila WipA
ComponentsWipA
KeywordsPEPTIDE BINDING PROTEIN / phosphotase
Function / homology: / WipA, alpha-helical hairpin / : / WipA-like, phosphatase domain / Metallo-dependent phosphatase-like / phosphatase activity / metal ion binding / IODIDE ION / WipA
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.554 Å
AuthorsXie, W. / Jia, Q.
Funding support China, 3items
OrganizationGrant numberCountry
Fundamental Research Funds for the Central Universities16lgjc76 China
the Science and Technology Program of Guangzhou201504010025 China
the Science and Technology Program of Guangzhou201605030012 China
CitationJournal: Acta Biochim. Biophys. Sin. (Shanghai) / Year: 2018
Title: Legionella pneumophila effector WipA, a bacterial PPP protein phosphatase with PTP activity
Authors: Jia, Q. / Lin, Y. / Gou, X. / He, L. / Shen, D. / Chen, D. / Xie, W. / Lu, Y.
History
DepositionAug 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WipA
B: WipA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7567
Polymers96,1212
Non-polymers6355
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, PISA server
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-11 kcal/mol
Surface area33850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.608, 95.976, 106.635
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein WipA


Mass: 48060.691 Da / Num. of mol.: 2 / Fragment: UNP residues 1-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: wipA / Production host: Escherichia coli (E. coli) / References: UniProt: Q5GA16
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.49 Å3/Da / Density % sol: 50.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 14% PEG6000, 0.1 M MES (pH 6.0) and 0.1 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 31780 / % possible obs: 100 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.25 / Net I/σ(I): 16
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.991 / Mean I/σ(I) obs: 2 / Num. unique obs: 31604 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N6X

5n6x


Resolution: 2.554→46.608 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.92
RfactorNum. reflection% reflection
Rfree0.2821 1517 4.8 %
Rwork0.2232 --
obs0.226 31604 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.554→46.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6267 0 6 75 6348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076401
X-RAY DIFFRACTIONf_angle_d0.8758707
X-RAY DIFFRACTIONf_dihedral_angle_d16.1333811
X-RAY DIFFRACTIONf_chiral_restr0.053986
X-RAY DIFFRACTIONf_plane_restr0.0051130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5543-2.63680.27591250.22852585X-RAY DIFFRACTION96
2.6368-2.7310.2961380.23772723X-RAY DIFFRACTION100
2.731-2.84030.34171270.23732736X-RAY DIFFRACTION100
2.8403-2.96960.30921520.24532685X-RAY DIFFRACTION100
2.9696-3.12610.33021640.24832697X-RAY DIFFRACTION100
3.1261-3.32190.3168950.23832758X-RAY DIFFRACTION100
3.3219-3.57830.27961600.22472717X-RAY DIFFRACTION100
3.5783-3.93830.26911150.21292773X-RAY DIFFRACTION100
3.9383-4.50770.25241560.20712758X-RAY DIFFRACTION100
4.5077-5.67770.29671450.21942785X-RAY DIFFRACTION100
5.6777-46.61610.261400.22142870X-RAY DIFFRACTION98

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