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- PDB-5nqp: Structure of a fHbp(V1.4):PorA(P1.16) chimera. Fusion at fHbp pos... -

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Basic information

Entry
Database: PDB / ID: 5nqp
TitleStructure of a fHbp(V1.4):PorA(P1.16) chimera. Fusion at fHbp position 151.
ComponentsFactor H binding protein variant B16_001,Major outer membrane protein P.IA,Factor H binding protein variant B16_001
KeywordsIMMUNE SYSTEM / Meningitis / Vaccine / Complement / Chimeric
Function / homology
Function and homology information


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. / Gram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / : / Porin domain superfamily / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Major outer membrane protein P.IA / Factor H binding protein variant B16_001
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
Neisseria meningitidis serogroup C (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsJohnson, S. / Hollingshead, S. / 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 20, 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 variant B16_001,Major outer membrane protein P.IA,Factor H binding protein variant B16_001
A: Factor H binding protein variant B16_001,Major outer membrane protein P.IA,Factor H binding protein variant B16_001
B: Factor H binding protein variant B16_001,Major outer membrane protein P.IA,Factor H binding protein variant B16_001
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,41421
Polymers88,3013
Non-polymers1,11318
Water50428
1
C: Factor H binding protein variant B16_001,Major outer membrane protein P.IA,Factor H binding protein variant B16_001
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,97310
Polymers29,4341
Non-polymers5399
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Factor H binding protein variant B16_001,Major outer membrane protein P.IA,Factor H binding protein variant B16_001
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7256
Polymers29,4341
Non-polymers2915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Factor H binding protein variant B16_001,Major outer membrane protein P.IA,Factor H binding protein variant B16_001
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7165
Polymers29,4341
Non-polymers2824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.720, 171.420, 131.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Factor H binding protein variant B16_001,Major outer membrane protein P.IA,Factor H binding protein variant B16_001 / Factor H binding protein variant B16_002 / Factor H binding protein variant B16_003 / Factor H ...Factor H binding protein variant B16_002 / Factor H binding protein variant B16_003 / Factor H binding protein variant B16_004 / Factor H binding protein variant B16_005 / Factor H binding protein variant B16_006 / Putative lipoprotein / Protein IA / Class 1 protein / Factor H binding protein variant B16_002 / Factor H binding protein variant B16_003 / Factor H binding protein variant B16_004 / Factor H binding protein variant B16_005 / Factor H binding protein variant B16_006 / Putative lipoprotein


Mass: 29433.740 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria), (gene. exp.) Neisseria meningitidis serogroup C (bacteria)
Gene: fhbp, porA / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Variant (production host): B834 / References: UniProt: Q6VS06, UniProt: P13415
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.2 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.15M sodium citrate, 2.0M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.86→40.75 Å / Num. obs: 26403 / % possible obs: 99.1 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.038 / Net I/σ(I): 17.1
Reflection shellResolution: 2.86→2.93 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 2 / Num. unique obs: 1923 / Rpim(I) all: 0.34 / % possible all: 99.4

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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: 2.86→40.745 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.78
RfactorNum. reflection% reflection
Rfree0.2391 1238 4.69 %
Rwork0.1984 --
obs0.2003 26375 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.86→40.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5916 0 63 28 6007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026045
X-RAY DIFFRACTIONf_angle_d0.5848114
X-RAY DIFFRACTIONf_dihedral_angle_d11.4023645
X-RAY DIFFRACTIONf_chiral_restr0.046899
X-RAY DIFFRACTIONf_plane_restr0.0031067
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.86-2.97450.35111340.30272746X-RAY DIFFRACTION99
2.9745-3.10980.34661040.28682806X-RAY DIFFRACTION99
3.1098-3.27370.29821650.26142720X-RAY DIFFRACTION99
3.2737-3.47870.29911380.23092738X-RAY DIFFRACTION98
3.4787-3.74710.26081140.21372807X-RAY DIFFRACTION98
3.7471-4.12390.23871430.19012756X-RAY DIFFRACTION99
4.1239-4.71990.21861100.15082836X-RAY DIFFRACTION99
4.7199-5.94360.19481580.16812811X-RAY DIFFRACTION99
5.9436-40.74880.21031720.18962917X-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)
12.77-2.87030.92014.7113-2.00381.1084-0.3337-0.32640.27250.62840.36770.5013-0.4385-0.3580.03270.80890.05050.2160.4522-0.05151.0232-18.6889-13.8563-20.9247
26.9163-0.4965-0.29364.8943-0.38222.3439-0.1659-0.284-0.10680.46250.1707-0.01940.13540.1806-0.01050.61810.04180.05020.2871-0.010.57890.1058-32.5773-20.7294
31.32972.19860.46048.01161.08031.0786-0.12720.0341-0.35060.53210.1994-0.23150.02120.09040.01730.6393-0.0484-0.04960.44730.10360.9702-26.135-83.7112-16.8565
42.52850.34980.45544.6431-0.65862.66690.0138-0.0702-0.2520.4716-0.0673-0.8677-0.60010.21730.10370.8454-0.1487-0.14640.37870.08170.8605-18.8687-58.176-17.7331
57.5086-1.7291-1.12581.06040.65051.0009-0.14940.81450.0332-0.2706-0.0070.04-0.51270.0830.13380.9715-0.2477-0.0190.5930.03530.4768-40.4893-52.4509-45.374
64.48570.28980.6694.679-0.78821.8361-0.10470.821-0.3216-0.1009-0.1721-0.8734-0.50160.78320.2580.8253-0.39950.1960.9023-0.07860.7806-15.3874-60.1505-41.5347
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 322 )
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 201 )
4X-RAY DIFFRACTION4chain 'A' and (resid 202 through 322 )
5X-RAY DIFFRACTION5chain 'B' and (resid 80 through 201 )
6X-RAY DIFFRACTION6chain 'B' and (resid 202 through 321 )

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