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

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Basic information

Entry
Database: PDB / ID: 5nqz
TitleStructure of a fHbp(V1.1):PorA(P1.16) chimera. Fusion at fHbp position 309.
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. / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / 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: 1.63 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 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,37820
Polymers58,2552
Non-polymers1,12318
Water9,728540
1
A: Factor H binding protein,Major outer membrane protein P.IA,Factor H binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,87713
Polymers29,1281
Non-polymers75012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Factor H binding protein,Major outer membrane protein P.IA,Factor H binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5017
Polymers29,1281
Non-polymers3736
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.370, 76.270, 83.900
Angle α, β, γ (deg.)90.00, 91.26, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A78 - 339
2010B78 - 339

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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: 29127.508 Da / Num. of mol.: 2
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
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / 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: 2.49 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.01M zinc chloride, 0.1M sodium acetate, 20%(w/v) PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92818 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92818 Å / Relative weight: 1
ReflectionResolution: 1.63→58.55 Å / Num. obs: 70772 / % possible obs: 98.6 % / Redundancy: 3 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.041 / Net I/σ(I): 12.7
Reflection shellResolution: 1.63→1.67 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4967 / Rpim(I) all: 0.534 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ayd

4ayd


Resolution: 1.63→58.55 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.93 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.085 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1944 3445 4.9 %RANDOM
Rwork0.16199 ---
obs0.16353 67325 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.699 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å20.01 Å2
2---0.72 Å2-0 Å2
3----0.46 Å2
Refinement stepCycle: 1 / Resolution: 1.63→58.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4046 0 45 540 4631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0194139
X-RAY DIFFRACTIONr_bond_other_d0.0080.023964
X-RAY DIFFRACTIONr_angle_refined_deg1.9751.955554
X-RAY DIFFRACTIONr_angle_other_deg1.44639124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9395528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56725.077195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59215729
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0481518
X-RAY DIFFRACTIONr_chiral_restr0.1680.2603
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024804
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02950
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7822.1942126
X-RAY DIFFRACTIONr_mcbond_other2.6372.1882117
X-RAY DIFFRACTIONr_mcangle_it3.8993.2682644
X-RAY DIFFRACTIONr_mcangle_other3.9073.272645
X-RAY DIFFRACTIONr_scbond_it4.3122.8342013
X-RAY DIFFRACTIONr_scbond_other4.3122.8342013
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7534.0172911
X-RAY DIFFRACTIONr_long_range_B_refined10.2319.8064527
X-RAY DIFFRACTIONr_long_range_B_other10.2319.8154528
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 29158 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.63→1.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 225 -
Rwork0.289 4735 -
obs--93.64 %

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