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- PDB-5x1u: Structure of the cytosolic domain of DotM derived from Legionella... -

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Basic information

Entry
Database: PDB / ID: 5x1u
TitleStructure of the cytosolic domain of DotM derived from Legionella pneumophila
ComponentsUncharacterized protein
KeywordsPROTEIN TRANSPORT / Type IV secretion system / Coupling protein complex / Effector translocation
Function / homology: / membrane / Phosphoesterase
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsKwak, M.J. / Kim, Y.G. / Oh, B.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation of Korea (NRF)2008-0061987 Korea, Republic Of
CitationJournal: Nat Microbiol / Year: 2017
Title: Architecture of the type IV coupling protein complex of Legionella pneumophila
Authors: Kwak, M.J. / Kim, J.D. / Kim, H. / Kim, C. / Bowman, J.W. / Kim, S. / Joo, K. / Lee, J. / Jin, K.S. / Kim, Y.G. / Lee, N.K. / Jung, J.U. / Oh, B.H.
History
DepositionJan 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 20, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Oct 30, 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

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)48,2432
Polymers48,2432
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-7 kcal/mol
Surface area19710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.529, 72.021, 65.691
Angle α, β, γ (deg.)90.000, 102.150, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein


Mass: 24121.496 Da / Num. of mol.: 2 / Fragment: UNP residues 158-365
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (strain Lens) (bacteria)
Strain: Lens / Gene: dotM, icmP, lpl0487 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5WZ95
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.45 Å3/Da / Density % sol: 49.75 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM Tris-HCl (pH8.5), 17%(v/v) PEG3350, 200mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 70306 / % possible obs: 91 % / Redundancy: 4.3 % / Biso Wilson estimate: 14.69 Å2 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.036 / Rrim(I) all: 0.088 / Χ2: 1.86 / Net I/σ(I): 9.1 / Num. measured all: 169586
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.832.60.17915290.9280.1110.2130.82472
1.83-1.862.60.17215840.910.1070.2040.84473.9
1.86-1.92.70.16616410.9180.1020.1960.87777.8
1.9-1.943.10.15617620.9410.0910.1820.89881.3
1.94-1.983.30.14718060.9550.0810.1690.94885.8
1.98-2.033.40.1418570.9620.0770.161.00286.7
2.03-2.083.60.13318990.9750.0710.1521.1489.7
2.08-2.133.80.12719310.9690.0660.1441.2290.8
2.13-2.23.90.1219790.980.0620.1351.37591.7
2.2-2.2740.11219890.9590.0580.1271.37493.8
2.27-2.353.90.10520070.9840.0540.1191.54193.6
2.35-2.444.10.120230.9840.0510.1121.62694.6
2.44-2.554.70.09920700.9880.0470.111.66996.8
2.55-2.6950.09520900.9930.0440.1051.85697.5
2.69-2.865.10.08921010.990.040.0981.88397.7
2.86-3.085.30.08220920.9940.0370.091.95298.6
3.08-3.395.10.07421360.9940.0340.0822.198.4
3.39-3.885.90.06321540.9960.0270.0692.09499.5
3.88-4.886.60.0621450.9970.0250.0652.26799.4
4.88-506.20.07722030.9960.0320.0844.14499.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
HKLdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→40.736 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.78 / Phase error: 17.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1983 2503 3.56 %
Rwork0.1756 67803 -
obs0.1764 70306 83.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.58 Å2 / Biso mean: 19.8341 Å2 / Biso min: 7.21 Å2
Refinement stepCycle: final / Resolution: 1.8→40.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3156 0 0 132 3288
Biso mean---21.58 -
Num. residues----398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073225
X-RAY DIFFRACTIONf_angle_d0.8294364
X-RAY DIFFRACTIONf_chiral_restr0.049476
X-RAY DIFFRACTIONf_plane_restr0.006564
X-RAY DIFFRACTIONf_dihedral_angle_d14.1611970
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.83460.1788930.16812601269458
1.8346-1.87210.1884960.17432686278259
1.8721-1.91280.20951030.16892881298464
1.9128-1.95730.24651210.17473194331571
1.9573-2.00620.21381250.18383437356276
2.0062-2.06050.20531280.17113473360178
2.0605-2.12110.18391370.17463686382381
2.1211-2.18960.20451380.17483766390484
2.1896-2.26780.20191450.17483850399586
2.2678-2.35860.2331460.17643848399486
2.3586-2.46590.22041500.17744040419089
2.4659-2.59590.18061530.18874151430492
2.5959-2.75850.19931550.19044255441094
2.7585-2.97140.21061630.1984288445196
2.9714-3.27040.22281560.1934330448696
3.2704-3.74330.20171630.18034387455098
3.7433-4.71510.15911660.14784450461699
4.7151-40.74630.19161650.16324480464599

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