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- PDB-8qk8: Structure of Legionella pneumophila Lcl C-terminal domain bound t... -

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Basic information

Entry
Database: PDB / ID: 8qk8
TitleStructure of Legionella pneumophila Lcl C-terminal domain bound to sulphate
ComponentsHbP1
KeywordsCELL ADHESION / Lcl / T2SS / adhesion / biofilm / Legionella pneumophila / collagen
Function / homologyProtein of unknown function DUF1566 / Lcl C-terminal domain / : / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / extracellular region / HbP1
Function and homology information
Biological speciesLegionella pneumophila 130b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRehman, S. / Garnett, J.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/M009920/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/R017662/1 United Kingdom
CitationJournal: Biorxiv / Year: 2023
Title: The Legionella collagen-like protein employs a unique binding mechanism for the recognition of host glycosaminoglycans.
Authors: Rehman, S. / Antonovic, A.K. / McIntire, I.E. / Zheng, H. / Cleaver, L. / Adams, C.O. / Portlock, T. / Richardson, K. / Shaw, R. / Oregioni, A. / Mastroianni, G. / Whittaker, S.B. / Kelly, G. ...Authors: Rehman, S. / Antonovic, A.K. / McIntire, I.E. / Zheng, H. / Cleaver, L. / Adams, C.O. / Portlock, T. / Richardson, K. / Shaw, R. / Oregioni, A. / Mastroianni, G. / Whittaker, S.B. / Kelly, G. / Fornili, A. / Cianciotto, N.P. / Garnett, J.A.
History
DepositionSep 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HbP1
B: HbP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3374
Polymers37,1452
Non-polymers1922
Water3,495194
1
A: HbP1
hetero molecules

A: HbP1
hetero molecules

A: HbP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2949
Polymers55,7183
Non-polymers5766
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area5310 Å2
ΔGint-61 kcal/mol
Surface area15970 Å2
MethodPISA
2
B: HbP1

B: HbP1

B: HbP1


Theoretical massNumber of molelcules
Total (without water)55,7183
Polymers55,7183
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area5210 Å2
ΔGint-59 kcal/mol
Surface area16040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.910, 74.910, 94.970
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11B-499-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: PHE / End label comp-ID: PHE / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 256 - 386 / Label seq-ID: 35 - 165

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein HbP1


Mass: 18572.584 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila 130b (bacteria) / Gene: hbP1 / Production host: Escherichia coli (E. coli) / References: UniProt: E7BLH6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.07 Å3/Da / Density % sol: 40.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% (v/v) glycerol, 20% (w/v) polyethylene glycol (PEG) 4000, 30 mM NaNO3, 30 mM Na2HPO4, 30 mM (NH4)2SO4, 100 mM bicine, 100 mM tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.9→64.91 Å / Num. obs: 24856 / % possible obs: 100 % / Redundancy: 19.3 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 28.7
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 1235 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→64.874 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.184 / WRfactor Rwork: 0.161 / Average fsc free: 0.9754 / Average fsc work: 0.9835 / Cross valid method: FREE R-VALUE / ESU R: 0.122 / ESU R Free: 0.112
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1874 1200 4.828 %
Rwork0.1604 23654 -
all0.162 --
obs-24854 99.968 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.968 Å2
Baniso -1Baniso -2Baniso -3
1-0.222 Å20.111 Å20 Å2
2--0.222 Å20 Å2
3----0.721 Å2
Refinement stepCycle: LAST / Resolution: 1.9→64.874 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 0 10 194 2262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0112112
X-RAY DIFFRACTIONr_bond_other_d0.0020.0161940
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.6392868
X-RAY DIFFRACTIONr_angle_other_deg0.7611.5894434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7995260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.635514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45410338
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.37710104
X-RAY DIFFRACTIONr_chiral_restr0.0650.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022602
X-RAY DIFFRACTIONr_gen_planes_other0.010.02538
X-RAY DIFFRACTIONr_nbd_refined0.1980.2399
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.21798
X-RAY DIFFRACTIONr_nbtor_refined0.180.21036
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21160
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2156
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1680.212
X-RAY DIFFRACTIONr_nbd_other0.2320.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1580.219
X-RAY DIFFRACTIONr_mcbond_it2.2272.5471046
X-RAY DIFFRACTIONr_mcbond_other2.2262.5461046
X-RAY DIFFRACTIONr_mcangle_it3.1384.561304
X-RAY DIFFRACTIONr_mcangle_other3.1384.5591305
X-RAY DIFFRACTIONr_scbond_it3.8312.9151066
X-RAY DIFFRACTIONr_scbond_other3.8112.9091059
X-RAY DIFFRACTIONr_scangle_it5.7435.1441564
X-RAY DIFFRACTIONr_scangle_other5.7145.1341553
X-RAY DIFFRACTIONr_lrange_it6.79126.1822444
X-RAY DIFFRACTIONr_lrange_other6.72624.9952400
X-RAY DIFFRACTIONr_ncsr_local_group_10.0730.054358
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.072510.05009
12AX-RAY DIFFRACTIONLocal ncs0.072510.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.9-1.9490.249930.18817330.19118290.9630.97799.8360.158
1.949-2.0030.195720.17516730.17617450.9680.9811000.148
2.003-2.0610.199560.15916660.1617220.9790.9841000.137
2.061-2.1240.236790.16415840.16716630.9680.9831000.14
2.124-2.1940.2141000.16215320.16516320.9720.9841000.142
2.194-2.2710.252640.16514930.16815570.9610.9841000.147
2.271-2.3560.212890.16113980.16414880.9710.98599.93280.144
2.356-2.4520.19790.16613960.16714750.980.9841000.15
2.452-2.5610.175760.16913300.1714060.980.9831000.155
2.561-2.6860.166590.1612900.1613500.9850.98499.92590.146
2.686-2.8310.223560.16212130.16412690.9740.9841000.153
2.831-3.0020.162640.15511580.15512220.9820.9861000.152
3.002-3.2090.229380.16111060.16311440.9720.9841000.162
3.209-3.4660.165520.16710180.16710700.9830.9831000.171
3.466-3.7950.227580.1519390.1559970.9760.9871000.16
3.795-4.2420.164570.1468380.1478960.9840.98699.88840.161
4.242-4.8940.122370.1377720.1368090.9930.991000.157
4.894-5.9860.142390.176540.1686930.9890.9871000.195
5.986-8.4290.213250.1715300.1735550.9790.9821000.195
8.429-64.8740.13570.1783300.1773380.9710.97299.70410.223

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