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- PDB-4r0g: Crystal structure of Lpg0393 from Legionella pneumophila -

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Basic information

Entry
Database: PDB / ID: 4r0g
TitleCrystal structure of Lpg0393 from Legionella pneumophila
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Vps9 / GEF
Function / homologyLpg0393, helical bundle domain / Helical bundle domain / HBD domain-containing protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsSohn, Y.S. / Shin, H.C. / Oh, B.H.
CitationJournal: Plos One / Year: 2015
Title: Lpg0393 of Legionella pneumophila Is a Guanine-Nucleotide Exchange Factor for Rab5, Rab21 and Rab22
Authors: Sohn, Y.S. / Shin, H.C. / Park, W.S. / Ge, J. / Kim, C.H. / Lee, B.L. / Heo, W.D. / Jung, J.U. / Rigden, D.J. / Oh, B.H.
History
DepositionJul 31, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
C: Uncharacterized protein
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)133,8294
Polymers133,8294
Non-polymers00
Water00
1
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)66,9152
Polymers66,9152
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-16 kcal/mol
Surface area24780 Å2
MethodPISA
2
C: Uncharacterized protein
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)66,9152
Polymers66,9152
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-16 kcal/mol
Surface area25440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.636, 111.706, 167.958
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAUTHOR DETERMINED BIOLOGICAL ASSEMBLY: UNKNOWN

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Components

#1: Protein
Uncharacterized protein / Lpg0393 protein


Mass: 33457.371 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Gene: lpg0393 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) RIL / References: UniProt: Q5ZYH9

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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: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 8% PEG 8000, 0.1M HEPES, 8% ethylene glycol, 13% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 61472 / Num. obs: 43800 / % possible obs: 99.7 % / Redundancy: 6.1 % / Rsym value: 0.057 / Net I/σ(I): 24.5
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.7 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.1_1168refinement
RefinementMethod to determine structure: SAD / Resolution: 2.7→34.039 Å / FOM work R set: 0.7736 / SU ML: 0.46 / σ(F): 1.82 / Phase error: 29.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2689 1899 5.14 %random
Rwork0.2215 ---
obs0.2239 36978 --
all-47766 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 170.96 Å2 / Biso mean: 79.96 Å2 / Biso min: 30.24 Å2
Refinement stepCycle: LAST / Resolution: 2.7→34.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8043 0 0 0 8043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018229
X-RAY DIFFRACTIONf_angle_d1.26811166
X-RAY DIFFRACTIONf_chiral_restr0.0891275
X-RAY DIFFRACTIONf_plane_restr0.0051390
X-RAY DIFFRACTIONf_dihedral_angle_d17.4792948
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7001-2.76760.39711020.36571975207770
2.7676-2.84240.36571080.32532088219674
2.8424-2.92590.34071390.29712118225776
2.9259-3.02030.31871260.28442216234280
3.0203-3.12820.33221250.2742320244583
3.1282-3.25340.34381460.26982437258387
3.2534-3.40130.3061430.2562524266790
3.4013-3.58040.32011250.24312597272292
3.5804-3.80450.27341500.23322767291797
3.8045-4.09780.28711390.2132688282795
4.0978-4.50930.24891520.18822763291597
4.5093-5.15990.21741370.17562826296398
5.1599-6.49350.25721630.20962845300898
6.4935-34.04210.21071440.18772912305696

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