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- PDB-4hfv: Crystal structure of lpg1851 protein from Legionella pneumophila ... -

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Basic information

Entry
Database: PDB / ID: 4hfv
TitleCrystal structure of lpg1851 protein from Legionella pneumophila (putative T4SS effector)
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Midwest Center for Structural Genomics / MCSG / effector
Function / homology
Function and homology information


de novo design (two linked rop proteins) - #330 / Substrate of the Dot/Icm secretion system / Putative substrate of the Dot/Icm secretion system / Substrate of the Dot/Icm secretion system, putative / de novo design (two linked rop proteins) / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix non-globular / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRIC ACID / SUCCINIC ACID / Uncharacterized protein
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.901 Å
AuthorsMichalska, K. / Xu, X. / Cui, H. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
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
DepositionOct 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5233
Polymers22,2131
Non-polymers3102
Water3,549197
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0466
Polymers44,4262
Non-polymers6204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area3450 Å2
ΔGint-4 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.339, 43.339, 205.621
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein Uncharacterized protein


Mass: 22213.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / Gene: lpg1851 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q5ZUE7
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2 M diammonium citrate, 20% PEG3350, 1/70 thermolysin, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794534 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2012 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794534 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 18726 / Num. obs: 18684 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 13.4
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.06 / Num. unique all: 899 / % possible all: 99.2

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
autoSHARPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.901→27.723 Å / SU ML: 0.2 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.19 / Stereochemistry target values: ML
Details: HYDROGEN ATOMS HAVE BEEN ADDED AT RIDING POSITIONS, THE PROTEIN WAS SUBJECTED TO IN SITU PROTEOLYSIS, THEREFORE THE EXACT LENGTH OF THE CRYSTALLIZED POLYPEPTIDE COULD NOT BE DETERMINED
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 951 5.11 %random
Rwork0.1829 ---
all0.1854 18596 --
obs0.1854 18596 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.901→27.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1553 0 21 197 1771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151663
X-RAY DIFFRACTIONf_angle_d1.362250
X-RAY DIFFRACTIONf_dihedral_angle_d17.48655
X-RAY DIFFRACTIONf_chiral_restr0.08248
X-RAY DIFFRACTIONf_plane_restr0.007293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.901-2.00120.28391470.25032429X-RAY DIFFRACTION100
2.0012-2.12660.26421550.20762452X-RAY DIFFRACTION100
2.1266-2.29070.27571350.20992491X-RAY DIFFRACTION100
2.2907-2.52110.22741320.17522484X-RAY DIFFRACTION100
2.5211-2.88560.24211270.1742537X-RAY DIFFRACTION100
2.8856-3.63420.22211250.18272542X-RAY DIFFRACTION100
3.6342-27.72550.20761300.16532710X-RAY DIFFRACTION99
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)
14.8141-2.23711.58712.88242.01187.714-0.6403-0.00541.1762-0.39380.4457-0.0273-1.25260.6530.13220.32670.0237-0.03620.2598-0.01650.2979-4.31855.561212.763
21.0824-0.8111-0.33631.04280.47170.9291-0.07950.1493-0.6202-0.3779-0.1150.51640.1032-0.19820.01520.1327-0.01710.00360.1022-0.0420.1357-1.6961-13.03324.1502
33.0823-2.74650.07723.88910.79375.6533-0.18770.0253-1.13450.3494-0.21470.6310.9396-0.72890.55670.2894-0.0270.08440.1488-0.14310.31360.2968-24.2239-2.3877
42.7655-0.86782.83451.863-0.44046.78320.1876-0.1791-0.79250.0856-0.03410.40950.6965-0.96350.4940.5-0.03310.0850.2154-0.0510.2884-1.0564-23.06246.9704
51.08230.4882-0.38331.9964-0.2712.694-0.110.1766-0.16080.0098-0.02740.22941.1714-0.4658-0.0296-0.0648-0.04840.03660.1980.01880.1188-3.7894-14.514915.7876
60.96910.87050.81551.65870.22051.5356-0.01670.1310.0816-0.06040.0035-0.0072-0.1405-0.1252-0.00360.0939-0.0006-0.00270.10230.00480.07925.0029-4.353411.7816
77.9361-1.621.83430.52120.10251.86910.18610.9260.87980.0861-0.5422-0.0255-1.64070.242-0.40660.4508-0.00420.02550.1468-0.02390.11420.74676.90410.036
80.5944-0.2193-0.41910.7269-0.30283.50140.167-0.04520.18070.0624-0.30810.5326-0.684-0.0529-0.17660.16360.00120.00030.181-0.03530.1069-2.4238-2.097924.3625
91.4171-0.58640.42090.8752-0.23410.5545-0.0349-0.44910.05830.34020.06370.03620.5929-0.0068-0.01220.254-0.03920.04210.2241-0.02880.144-2.0031-18.280929.5647
102.405-0.6917-1.11854.63360.10192.13730.1050.11130.38980.35460.1067-0.8081-0.39930.02590.0050.1549-0.01150.00260.1776-0.00670.14015.2755.993529.3459
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 : 7 )
2X-RAY DIFFRACTION2chain 'A' and (resid 8 : 26 )
3X-RAY DIFFRACTION3chain 'A' and (resid 27 : 33 )
4X-RAY DIFFRACTION4chain 'A' and (resid 34 : 45 )
5X-RAY DIFFRACTION5chain 'A' and (resid 46 : 68 )
6X-RAY DIFFRACTION6chain 'A' and (resid 69 : 108 )
7X-RAY DIFFRACTION7chain 'A' and (resid 109 : 118 )
8X-RAY DIFFRACTION8chain 'A' and (resid 119 : 136 )
9X-RAY DIFFRACTION9chain 'A' and (resid 137 : 159 )
10X-RAY DIFFRACTION10chain 'A' and (resid 160 : 189 )

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