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- PDB-5nqx: Structure of a fHbp(V1.1):PorA(P1.16) chimera. Fusion at fHbp pos... -

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Basic information

Entry
Database: PDB / ID: 5nqx
TitleStructure of a fHbp(V1.1):PorA(P1.16) chimera. Fusion at fHbp position 294.
ComponentsFactor H binding protein,Major outer membrane protein P.IA,Factor H binding protein
KeywordsIMMUNE SYSTEM / Meningitis / Vaccine / Complement / Chimeric
Function / homology
Function and homology information


bacterial extracellular vesicle / porin activity / pore complex / cell outer membrane / monoatomic ion transmembrane transport
Similarity search - Function
Immunoglobulin-like - #1980 / Porin, Neisseria sp. type / Factor H binding protein, C-terminal / : / : / Factor H binding protein, C-terminal / Factor H binding protein, N-terminal / Porin - #90 / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. ...Immunoglobulin-like - #1980 / Porin, Neisseria sp. type / Factor H binding protein, C-terminal / : / : / Factor H binding protein, C-terminal / Factor H binding protein, N-terminal / Porin - #90 / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Porin domain, Gram-negative type / Gram-negative porin / Porin, Gram-negative type / : / Porin domain superfamily / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Major outer membrane protein P.IA / Factor H binding protein
Similarity search - Component
Biological speciesNeisseria meningitidis MC58 (bacteria)
Neisseria meningitidis serogroup C (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.66 Å
AuthorsJohnson, S. / Jongerius, I. / Lea, S.M. / Tang, C.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G0900888 United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: Structure-based design of chimeric antigens for multivalent protein vaccines.
Authors: Hollingshead, S. / Jongerius, I. / Exley, R.M. / Johnson, S. / Lea, S.M. / Tang, C.M.
History
DepositionApr 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Factor H binding protein,Major outer membrane protein P.IA,Factor H binding protein
A: Factor H binding protein,Major outer membrane protein P.IA,Factor H binding protein
B: Factor H binding protein,Major outer membrane protein P.IA,Factor H binding protein
D: Factor H binding protein,Major outer membrane protein P.IA,Factor H binding protein
E: Factor H binding protein,Major outer membrane protein P.IA,Factor H binding protein


Theoretical massNumber of molelcules
Total (without water)145,9235
Polymers145,9235
Non-polymers00
Water00
1
C: Factor H binding protein,Major outer membrane protein P.IA,Factor H binding protein


Theoretical massNumber of molelcules
Total (without water)29,1851
Polymers29,1851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Factor H binding protein,Major outer membrane protein P.IA,Factor H binding protein


Theoretical massNumber of molelcules
Total (without water)29,1851
Polymers29,1851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Factor H binding protein,Major outer membrane protein P.IA,Factor H binding protein


Theoretical massNumber of molelcules
Total (without water)29,1851
Polymers29,1851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Factor H binding protein,Major outer membrane protein P.IA,Factor H binding protein


Theoretical massNumber of molelcules
Total (without water)29,1851
Polymers29,1851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Factor H binding protein,Major outer membrane protein P.IA,Factor H binding protein


Theoretical massNumber of molelcules
Total (without water)29,1851
Polymers29,1851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.850, 114.900, 160.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein
Factor H binding protein,Major outer membrane protein P.IA,Factor H binding protein / Protein IA / Class 1 protein


Mass: 29184.555 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis MC58, (gene. exp.) Neisseria meningitidis serogroup C (bacteria)
Gene: NMB1870, porA / Variant: V1.1 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): B834 / References: UniProt: Q9JXV4, UniProt: P13415

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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: 2.97 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG4000, 0.3M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97858 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97858 Å / Relative weight: 1
ReflectionResolution: 3.66→81.65 Å / Num. obs: 19820 / % possible obs: 99.3 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.101 / Net I/σ(I): 7.6
Reflection shellResolution: 3.66→3.76 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.833 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1431 / Rpim(I) all: 0.439 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ayd

4ayd


Resolution: 3.66→81.636 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.08
RfactorNum. reflection% reflection
Rfree0.2815 975 4.93 %
Rwork0.2324 --
obs0.2348 19782 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.66→81.636 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9572 0 0 0 9572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029701
X-RAY DIFFRACTIONf_angle_d0.42413037
X-RAY DIFFRACTIONf_dihedral_angle_d11.9085846
X-RAY DIFFRACTIONf_chiral_restr0.0421450
X-RAY DIFFRACTIONf_plane_restr0.0021717
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6601-3.85310.3681210.32112650X-RAY DIFFRACTION100
3.8531-4.09450.32581390.29222630X-RAY DIFFRACTION99
4.0945-4.41060.25691520.21992657X-RAY DIFFRACTION100
4.4106-4.85440.23911300.19452669X-RAY DIFFRACTION99
4.8544-5.55670.31241530.21952649X-RAY DIFFRACTION99
5.5567-7.00020.30971310.23792727X-RAY DIFFRACTION100
7.0002-81.6560.2441490.21682825X-RAY DIFFRACTION98
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)
10.57790.1604-0.34180.4251-0.55760.9028-0.18720.0243-0.128-0.1453-0.00850.1296-0.4407-0.3576-0.01770.50880.06820.04690.75640.07720.9175-3.4422-7.1695-46.3915
20.10290.153-0.5111.899-1.04913.3355-0.3088-0.2733-0.40720.4475-0.02430.7423-0.4471-0.4375-1.11170.21640.05020.06860.65180.05810.8066-19.13868.9358-44.079
30.5696-0.07640.28551.00380.27930.5325-0.22660.23430.0970.16640.08220.21140.0896-0.47430.00020.526-0.070.17550.71440.02480.654-44.125-29.7756-58.51
40.5568-0.52220.35412.3130.60890.67510.03140.32120.35010.61430.10020.44940.1878-0.17070.34850.2102-0.05990.16470.66110.00090.601-60.263-17.016-47.6105
51.0590.2515-0.39990.1296-0.31140.6592-0.02640.1482-0.27650.36330.01950.38760.4744-0.31020.01590.5215-0.13340.12080.6135-0.06570.4118-23.3453-30.4202-98.241
60.9935-0.2358-0.93630.92040.01670.9175-0.1683-0.2152-0.02130.31950.13010.25710.6213-0.0654-0.05620.5568-0.09620.14330.70930.02090.7423-39.695-37.8392-84.922
71.7844-0.93740.42761.5785-0.63090.2544-0.3137-0.06870.14810.0953-0.0407-0.29360.59610.2695-2.29021.1864-0.03730.50060.6954-0.01180.61213.7522-35.2088-79.152
81.2740.7287-0.15570.573-0.70833.1651-0.72960.2023-0.0238-0.76840.454-0.23541.5891-0.4391-0.41221.0799-0.08960.22460.68080.030.8955-1.053-30.8553-61.5905
90.49570.63740.28171.1127-0.05180.7357-0.03070.03-0.10720.3976-0.1374-0.4915-0.287-0.3486-0.01410.56210.0044-0.01690.64840.03670.7045-31.5216-46.7066-33.2157
100.48710.28110.2640.2074-0.08342.7024-0.40840.248-0.017-0.0624-0.2576-0.6304-1.79990.7468-1.07350.9588-0.3555-0.23330.82180.16630.8962-15.9529-31.9396-25.429
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 79 through 201 )
2X-RAY DIFFRACTION2chain 'C' and (resid 202 through 321 )
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 201 )
4X-RAY DIFFRACTION4chain 'A' and (resid 202 through 321 )
5X-RAY DIFFRACTION5chain 'B' and (resid 79 through 201 )
6X-RAY DIFFRACTION6chain 'B' and (resid 202 through 321 )
7X-RAY DIFFRACTION7chain 'D' and (resid 79 through 201 )
8X-RAY DIFFRACTION8chain 'D' and (resid 202 through 321 )
9X-RAY DIFFRACTION9chain 'E' and (resid 79 through 201 )
10X-RAY DIFFRACTION10chain 'E' and (resid 202 through 321 )

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