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- PDB-5dgg: Central domain of uncharacterized Lpg1148 protein from Legionella... -

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Basic information

Entry
Database: PDB / ID: 5dgg
TitleCentral domain of uncharacterized Lpg1148 protein from Legionella pneumophila
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Legionella pneumophila / structural genomics / APC105518 / Midwest Center for Structural Genomics / MCSG / PSI-Biology
Function / homologyLegionella ubiquitin-specific protease A domain / Legionella ubiquitin-specific protease A domain / membrane => GO:0016020 / LupA domain-containing protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.93 Å
AuthorsOsipiuk, J. / Evdokimova, E. / Yim, V. / Joachimiak, A. / Ensminger, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
Funding support Canada, United States, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-13340 Canada
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
CitationJournal: Mol. Syst. Biol. / Year: 2016
Title: Diverse mechanisms of metaeffector activity in an intracellular bacterial pathogen, Legionella pneumophila.
Authors: Urbanus, M.L. / Quaile, A.T. / Stogios, P.J. / Morar, M. / Rao, C. / Di Leo, R. / Evdokimova, E. / Lam, M. / Oatway, C. / Cuff, M.E. / Osipiuk, J. / Michalska, K. / Nocek, B.P. / Taipale, M. ...Authors: Urbanus, M.L. / Quaile, A.T. / Stogios, P.J. / Morar, M. / Rao, C. / Di Leo, R. / Evdokimova, E. / Lam, M. / Oatway, C. / Cuff, M.E. / Osipiuk, J. / Michalska, K. / Nocek, B.P. / Taipale, M. / Savchenko, A. / Ensminger, A.W.
History
DepositionAug 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5525
Polymers42,4462
Non-polymers1063
Water2,720151
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2943
Polymers21,2231
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2582
Polymers21,2231
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.085, 56.564, 121.994
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein


Mass: 21222.781 Da / Num. of mol.: 2 / Fragment: UNP residues 212-310
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg1148 / Plasmid: pET15b / Details (production host): modified / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5ZWD7
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 1.99 Å3/Da / Density % sol: 38.34 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 2 M ammonium sulfate, 4% sucrose, 0.01 M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 9, 2015
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. all: 26237 / Num. obs: 26237 / % possible obs: 99.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.036 / Rrim(I) all: 0.086 / Χ2: 1.018 / Net I/av σ(I): 25.23 / Net I/σ(I): 8.3 / Num. measured all: 145864
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.93-1.964.90.7432.112950.7420.3720.8340.80799.3
1.96-25.20.65712480.7830.3180.7310.846100
2-2.045.20.60313080.8250.290.6710.868100
2.04-2.085.30.52312900.8840.2480.580.873100
2.08-2.125.40.42112800.9070.1980.4660.921100
2.12-2.175.50.39412950.9260.1850.4360.927100
2.17-2.235.60.31812860.9570.1470.3510.974100
2.23-2.295.70.30312930.9650.1380.3330.957100
2.29-2.365.80.2613120.9750.1170.2860.957100
2.36-2.435.90.21612860.9840.0960.2370.916100
2.43-2.525.80.1912960.9880.0850.2090.953100
2.52-2.625.90.16813070.9910.0750.1850.916100
2.62-2.745.80.12513150.9920.0560.1380.951100
2.74-2.885.80.09613120.9950.0430.1061.021100
2.88-3.065.80.07613130.9960.0340.0831.063100
3.06-3.35.80.06413200.9970.0290.071.197100
3.3-3.635.70.0613230.9960.0280.0671.344100
3.63-4.165.60.05613470.9970.0260.0621.365100
4.16-5.245.50.0413560.9990.0180.0441.31100
5.24-505.20.02914550.9990.0140.0321.07599.2

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.93→38.3 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 7.775 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2181 1327 5.1 %RANDOM
Rwork0.1755 ---
obs0.1777 24854 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.54 Å2 / Biso mean: 38.57 Å2 / Biso min: 18.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å2-0 Å20 Å2
2--0.4 Å20 Å2
3----0.55 Å2
Refinement stepCycle: final / Resolution: 1.93→38.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2767 0 3 151 2921
Biso mean--35.22 42.42 -
Num. residues----352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192907
X-RAY DIFFRACTIONr_bond_other_d0.0020.022725
X-RAY DIFFRACTIONr_angle_refined_deg1.541.9693972
X-RAY DIFFRACTIONr_angle_other_deg0.82936309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4965374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.50224.681141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.57915485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0791516
X-RAY DIFFRACTIONr_chiral_restr0.0840.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213325
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02641
X-RAY DIFFRACTIONr_mcbond_it2.062.5641430
X-RAY DIFFRACTIONr_mcbond_other2.0582.5631429
X-RAY DIFFRACTIONr_mcangle_it3.0593.8221787
LS refinement shellResolution: 1.929→1.979 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 76 -
Rwork0.256 1694 -
all-1770 -
obs--92.04 %
Refinement TLS params.

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 °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.98120.19480.31540.57410.25351.1986-0.05970.0901-0.1760.11510.10480.0605-0.03140.1702-0.04520.05420.01240.00370.0971-0.01560.0538-5.237-12.406413.1358
20.94950.0866-0.00941.992-0.11141.0598-0.0281-0.1160.0794-0.10920.21650.28190.03110.0352-0.18840.0637-0.0173-0.02130.05930.03470.1-20.254715.994515.6286
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A123 - 304
2X-RAY DIFFRACTION2B123 - 306

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