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- PDB-8q4e: Structure of Legionella pneumophila Lcl C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 8q4e
TitleStructure of Legionella pneumophila Lcl C-terminal domain
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) / HbP1
Function and homology information
Biological speciesLegionella pneumophila 130b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 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
DepositionAug 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HbP1
B: HbP1
C: HbP1


Theoretical massNumber of molelcules
Total (without water)56,4213
Polymers56,4213
Non-polymers00
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.600, 52.870, 97.270
Angle α, β, γ (deg.)90.000, 112.090, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A

NCS domain segments:

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: 271 - 401 / Label seq-ID: 35 - 165

Dom-IDComponent-IDEns-ID
111
211
322
422
533
633

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6

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Components

#1: Protein HbP1


Mass: 18807.061 Da / Num. of mol.: 3
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.96 Å3/Da / Density % sol: 37.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 2.0 M (NH4)2SO4, 0.1 M bis-tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97969 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: 0.97969 Å / Relative weight: 1
ReflectionResolution: 1.9→45.56 Å / Num. obs: 34006 / % possible obs: 99.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 16.7
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 6.7 / Num. unique obs: 2460 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
xia2data reduction
Aimlessdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→45.56 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / Cross valid method: FREE R-VALUE / ESU R: 0.133 / ESU R Free: 0.119
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1878 1659 4.879 %
Rwork0.1582 32347 -
all0.16 --
obs-34006 99.328 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.818 Å2
Baniso -1Baniso -2Baniso -3
1--0.423 Å2-0 Å2-0.141 Å2
2---0.434 Å20 Å2
3---0.731 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3087 0 0 397 3484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0113156
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162910
X-RAY DIFFRACTIONr_angle_refined_deg1.181.6414284
X-RAY DIFFRACTIONr_angle_other_deg0.6511.596651
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.735390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.87521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85110489
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.5410156
X-RAY DIFFRACTIONr_chiral_restr0.0570.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023903
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02807
X-RAY DIFFRACTIONr_nbd_refined0.20.2572
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.22762
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21491
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21689
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2239
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1080.24
X-RAY DIFFRACTIONr_nbd_other0.1560.228
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2370.29
X-RAY DIFFRACTIONr_mcbond_it1.2190.8561569
X-RAY DIFFRACTIONr_mcbond_other1.2190.8561569
X-RAY DIFFRACTIONr_mcangle_it1.6691.531956
X-RAY DIFFRACTIONr_mcangle_other1.6691.531957
X-RAY DIFFRACTIONr_scbond_it2.8261.1471587
X-RAY DIFFRACTIONr_scbond_other2.8251.1471588
X-RAY DIFFRACTIONr_scangle_it4.3181.9492328
X-RAY DIFFRACTIONr_scangle_other4.3171.9492329
X-RAY DIFFRACTIONr_lrange_it6.23810.1533566
X-RAY DIFFRACTIONr_lrange_other6.1819.0893485
X-RAY DIFFRACTIONr_ncsr_local_group_10.0570.054424
X-RAY DIFFRACTIONr_ncsr_local_group_20.0550.054430
X-RAY DIFFRACTIONr_ncsr_local_group_30.0430.054453
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.056860.05011
12AX-RAY DIFFRACTIONLocal ncs0.056860.05011
23AX-RAY DIFFRACTIONLocal ncs0.055380.05011
24AX-RAY DIFFRACTIONLocal ncs0.055380.05011
35AX-RAY DIFFRACTIONLocal ncs0.04340.05011
36AX-RAY DIFFRACTIONLocal ncs0.04340.05011
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.2471030.1952352X-RAY DIFFRACTION97.0739
1.949-2.0030.2261250.1742307X-RAY DIFFRACTION99.8358
2.003-2.0610.1891120.1642254X-RAY DIFFRACTION99.8734
2.061-2.1240.1991060.1592224X-RAY DIFFRACTION99.7431
2.124-2.1930.212970.1512146X-RAY DIFFRACTION99.6889
2.193-2.270.194920.1532048X-RAY DIFFRACTION99.674
2.27-2.3560.2381000.1531989X-RAY DIFFRACTION99.5236
2.356-2.4520.1741020.1461915X-RAY DIFFRACTION99.7034
2.452-2.560.162870.1471838X-RAY DIFFRACTION99.4832
2.56-2.6850.1651040.1471736X-RAY DIFFRACTION99.5671
2.685-2.8290.207940.1631637X-RAY DIFFRACTION99.4828
2.829-30.1791030.1491580X-RAY DIFFRACTION99.8221
3-3.2060.168620.1561502X-RAY DIFFRACTION99.4911
3.206-3.4620.19760.1651393X-RAY DIFFRACTION99.2568
3.462-3.790.164680.151293X-RAY DIFFRACTION98.8381
3.79-4.2340.177630.151141X-RAY DIFFRACTION99.3399
4.234-4.8820.176470.1441034X-RAY DIFFRACTION99.2654
4.882-5.9620.187490.173882X-RAY DIFFRACTION99.3597
5.962-8.360.196430.184672X-RAY DIFFRACTION97.6776
8.36-45.560.2260.211404X-RAY DIFFRACTION98.1735
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)
11.7586-0.21690.31141.52890.43452.00880.02870.08330.1012-0.0345-0.0066-0.0162-0.01180.0421-0.02220.03640.0122-0.00440.00790.00080.0363-4.28842.37824.694
21.85630.3511-0.05521.4037-0.19592.46070.00220.0811-0.1087-0.0524-0.0087-0.09090.075-0.01630.00640.0141-0.0008-0.01280.0287-0.0020.042813.33127.43524.543
31.22630.0125-0.0472.0486-0.14252.41890.0180.0459-0.0654-0.04920.0140.1717-0.0434-0.0423-0.03210.0396-0.0127-0.02560.01380.00990.072-8.50219.64524.763
Refinement TLS groupSelection: ALL

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