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- PDB-2y7s: Structure of a designed meningococcal antigen (factor H binding p... -

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Basic information

Entry
Database: PDB / ID: 2y7s
TitleStructure of a designed meningococcal antigen (factor H binding protein, mutant G1) inducing broad protective immunity
ComponentsFACTOR H BINDING PROTEIN
KeywordsIMMUNE SYSTEM / ANTIGEN / EPITOPE / ANTIBODY / STRUCTURE-BASED DESIGN / VACCINE
Function / homology
Function and homology information


bacterial extracellular vesicle / cell outer membrane
Similarity search - Function
Immunoglobulin-like - #1980 / : / : / Factor H binding protein, N-terminal / Factor H binding protein, C-terminal / Factor H binding protein, C-terminal / Porin - #90 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Prokaryotic membrane lipoprotein lipid attachment site profile. ...Immunoglobulin-like - #1980 / : / : / Factor H binding protein, N-terminal / Factor H binding protein, C-terminal / Factor H binding protein, C-terminal / Porin - #90 / 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
Factor H binding protein
Similarity search - Component
Biological speciesNEISSERIA MENINGITIDIS SEROGROUP B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMalito, E. / Spraggon, G. / Bottomley, M.J.
CitationJournal: Sci.Transl.Med / Year: 2011
Title: Rational Design of a Meningococcal Antigen Inducing Broad Protective Immunity.
Authors: Scarselli, M. / Arico, B. / Brunelli, B. / Savino, S. / Di Marcello, F. / Palumbo, E. / Veggi, D. / Ciucchi, L. / Cartocci, E. / Bottomley, M.J. / Malito, E. / Lo Surdo, P. / Comanducci, M. ...Authors: Scarselli, M. / Arico, B. / Brunelli, B. / Savino, S. / Di Marcello, F. / Palumbo, E. / Veggi, D. / Ciucchi, L. / Cartocci, E. / Bottomley, M.J. / Malito, E. / Lo Surdo, P. / Comanducci, M. / Giuliani, M.M. / Cantini, F. / Dragonetti, S. / Colaprico, A. / Doro, F. / Giannetti, P. / Pallaoro, M. / Brogioni, B. / Tontini, M. / Hilleringmann, M. / Nardi-Dei, V. / Banci, L. / Pizza, M. / Rappuoli, R.
History
DepositionFeb 1, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references / Refinement description / Source and taxonomy
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FACTOR H BINDING PROTEIN
B: FACTOR H BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)55,4382
Polymers55,4382
Non-polymers00
Water10,251569
1
A: FACTOR H BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)27,7191
Polymers27,7191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FACTOR H BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)27,7191
Polymers27,7191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.480, 99.650, 58.060
Angle α, β, γ (deg.)90.00, 97.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FACTOR H BINDING PROTEIN


Mass: 27718.893 Da / Num. of mol.: 2 / Fragment: RESIDUES 73-320 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THE SEQUENCE OF FHBP CORRESPONDS TO VARIANT 1.1 WITH 23 MUTATIONS FROM VARIANTS 2 AND 3
Source: (gene. exp.) NEISSERIA MENINGITIDIS SEROGROUP B (bacteria)
Strain: MC58 / Variant: 1.1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9JXV4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 569 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ILE 199 TO LEU ENGINEERED RESIDUE IN CHAIN A, ALA 200 TO GLY ...ENGINEERED RESIDUE IN CHAIN A, ILE 199 TO LEU ENGINEERED RESIDUE IN CHAIN A, ALA 200 TO GLY ENGINEERED RESIDUE IN CHAIN A, SER 205 TO ALA ENGINEERED RESIDUE IN CHAIN A, ASP 207 TO ASN ENGINEERED RESIDUE IN CHAIN A, LYS 208 TO GLN ENGINEERED RESIDUE IN CHAIN A, GLU 211 TO ASP ENGINEERED RESIDUE IN CHAIN A, ARG 214 TO LYS ENGINEERED RESIDUE IN CHAIN A, THR 216 TO GLU ENGINEERED RESIDUE IN CHAIN A, ALA 238 TO THR ENGINEERED RESIDUE IN CHAIN A, ALA 239 TO LYS ENGINEERED RESIDUE IN CHAIN A, ASP 257 TO GLU ENGINEERED RESIDUE IN CHAIN A, ALA 260 TO SER ENGINEERED RESIDUE IN CHAIN A, ASP 262 TO GLU ENGINEERED RESIDUE IN CHAIN A, PRO 265 TO ALA ENGINEERED RESIDUE IN CHAIN A, ARG 269 TO SER ENGINEERED RESIDUE IN CHAIN A, SER 274 TO LEU ENGINEERED RESIDUE IN CHAIN A, SER 276 TO ASP ENGINEERED RESIDUE IN CHAIN A, LEU 278 TO ARG ENGINEERED RESIDUE IN CHAIN A, ASN 280 TO GLY ENGINEERED RESIDUE IN CHAIN A, GLN 281 TO SER ENGINEERED RESIDUE IN CHAIN A, ALA 282 TO GLU ENGINEERED RESIDUE IN CHAIN A, LYS 295 TO ARG ENGINEERED RESIDUE IN CHAIN B, ILE 199 TO LEU ENGINEERED RESIDUE IN CHAIN B, ALA 200 TO GLY ENGINEERED RESIDUE IN CHAIN B, SER 205 TO ALA ENGINEERED RESIDUE IN CHAIN B, ASP 207 TO ASN ENGINEERED RESIDUE IN CHAIN B, LYS 208 TO GLN ENGINEERED RESIDUE IN CHAIN B, GLU 211 TO ASP ENGINEERED RESIDUE IN CHAIN B, ARG 214 TO LYS ENGINEERED RESIDUE IN CHAIN B, THR 216 TO GLU ENGINEERED RESIDUE IN CHAIN B, ALA 238 TO THR ENGINEERED RESIDUE IN CHAIN B, ALA 239 TO LYS ENGINEERED RESIDUE IN CHAIN B, ASP 257 TO GLU ENGINEERED RESIDUE IN CHAIN B, ALA 260 TO SER ENGINEERED RESIDUE IN CHAIN B, ASP 262 TO GLU ENGINEERED RESIDUE IN CHAIN B, PRO 265 TO ALA ENGINEERED RESIDUE IN CHAIN B, ARG 269 TO SER ENGINEERED RESIDUE IN CHAIN B, SER 274 TO LEU ENGINEERED RESIDUE IN CHAIN B, SER 276 TO ASP ENGINEERED RESIDUE IN CHAIN B, LEU 278 TO ARG ENGINEERED RESIDUE IN CHAIN B, ASN 280 TO GLY ENGINEERED RESIDUE IN CHAIN B, GLN 281 TO SER ENGINEERED RESIDUE IN CHAIN B, ALA 282 TO GLU ENGINEERED RESIDUE IN CHAIN B, LYS 295 TO ARG

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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: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 6.6 / Details: 20% PEG 3350, 0.2M AMMONIUM FORMATE, PH 6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 41959 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 11.87 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.5 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W80

2w80


Resolution: 1.9→49.817 Å / SU ML: 0.24 / σ(F): 1.36 / Phase error: 22.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2327 2114 5 %
Rwork0.1856 --
obs0.1879 41959 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.31 Å2 / ksol: 0.299 e/Å3
Displacement parametersBiso mean: 14 Å2
Baniso -1Baniso -2Baniso -3
1-0.7971 Å20 Å2-2.587 Å2
2---1.529 Å20 Å2
3---0.7318 Å2
Refinement stepCycle: LAST / Resolution: 1.9→49.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3653 0 0 569 4222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073708
X-RAY DIFFRACTIONf_angle_d1.1174970
X-RAY DIFFRACTIONf_dihedral_angle_d12.8861388
X-RAY DIFFRACTIONf_chiral_restr0.078540
X-RAY DIFFRACTIONf_plane_restr0.003661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.901-1.94520.39881320.35142610X-RAY DIFFRACTION99
1.9452-1.99390.25661370.19982685X-RAY DIFFRACTION100
1.9939-2.04780.23651340.1752615X-RAY DIFFRACTION100
2.0478-2.10810.25521420.16572613X-RAY DIFFRACTION100
2.1081-2.17610.22051400.17852691X-RAY DIFFRACTION100
2.1761-2.25390.33631260.25352683X-RAY DIFFRACTION100
2.2539-2.34410.29551440.21842613X-RAY DIFFRACTION100
2.3441-2.45080.24611400.17882642X-RAY DIFFRACTION100
2.4508-2.580.23721510.18222645X-RAY DIFFRACTION100
2.58-2.74160.26931370.18432676X-RAY DIFFRACTION100
2.7416-2.95330.23871530.18392662X-RAY DIFFRACTION100
2.9533-3.25050.22151300.17092662X-RAY DIFFRACTION100
3.2505-3.72070.19931480.16452671X-RAY DIFFRACTION100
3.7207-4.68710.16571440.13642675X-RAY DIFFRACTION100
4.6871-49.83370.15241560.15182702X-RAY DIFFRACTION100

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