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- PDB-5xta: Crystal structure of lpg1832, a VirK family protein from Legionel... -

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Basic information

Entry
Database: PDB / ID: 5xta
TitleCrystal structure of lpg1832, a VirK family protein from Legionella pneumophila
ComponentsVirK protein
KeywordsOXIDOREDUCTASE / novel fold / type II secretion
Function / homologyUncharacterised protein family VirK / VirK protein / VirK family protein / VirK protein
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsYin, S. / Gong, X. / Zhang, N. / Ge, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31270770 China
National Natural Science Foundation of China31400641 China
CitationJournal: FEBS Lett. / Year: 2017
Title: Crystal structure of lpg1832, a VirK family protein from Legionella pneumophila, reveals a novel fold for bacterial VirK proteins
Authors: Zhang, N. / Yin, S. / Liu, S. / Sun, A. / Zhou, M. / Gong, X. / Ge, H.
History
DepositionJun 18, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: VirK protein
B: VirK protein
C: VirK protein
D: VirK protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4427
Polymers53,1584
Non-polymers2843
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7700 Å2
ΔGint-62 kcal/mol
Surface area20100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.200, 74.840, 85.150
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
VirK protein


Mass: 13289.414 Da / Num. of mol.: 4 / Fragment: UNP residues 19-138
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: A1D14_09105, ERS240560_00839, ERS253249_02394 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: A0A128ZU06, UniProt: Q5ZUG6*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M Bis-Tris pH 5.5, 25% w Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2→85 Å / Num. obs: 30567 / % possible obs: 93.3 % / Redundancy: 10.5 % / Net I/σ(I): 10.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
SCALAdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.201 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2601 1525 5 %RANDOM
Rwork0.21824 ---
obs0.22025 28974 93.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.851 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å2-0 Å2-0 Å2
2---1.17 Å20 Å2
3---2.65 Å2
Refinement stepCycle: 1 / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3660 0 16 261 3937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193774
X-RAY DIFFRACTIONr_bond_other_d00.023514
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.9855116
X-RAY DIFFRACTIONr_angle_other_deg3.74838166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0645490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.16924.717159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.26115596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.961520
X-RAY DIFFRACTIONr_chiral_restr0.0910.2600
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024209
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02743
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_it2.6063.4521930
X-RAY DIFFRACTIONr_mcbond_other2.6053.4511929
X-RAY DIFFRACTIONr_mcangle_it4.2635.1622409
X-RAY DIFFRACTIONr_mcangle_other4.2635.1622410
X-RAY DIFFRACTIONr_scbond_it3.443.931844
X-RAY DIFFRACTIONr_scbond_other3.4393.931844
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.515.7072701
X-RAY DIFFRACTIONr_long_range_B_refined7.87341.6963911
X-RAY DIFFRACTIONr_long_range_B_other7.82741.523869
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 124 -
Rwork0.279 2253 -
obs--99.87 %

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