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- PDB-7nru: Structure of a natural chimera of meningococcal factor H binding ... -

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Basic information

Entry
Database: PDB / ID: 7nru
TitleStructure of a natural chimera of meningococcal factor H binding protein belonging to NL096 strain
ComponentsFactor H binding protein variant 1-2,3.x
KeywordsPROTEIN BINDING / meningococcal antigen / natural chimera
Function / homologyFactor H binding protein, C-terminal / : / : / Factor H binding protein, C-terminal / Factor H binding protein, N-terminal / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / cell outer membrane / Factor H binding protein variant A62_001
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21998357323 Å
AuthorsVeggi, D. / Malito, E. / Bottomley, M.J.
Citation
Journal: Comput Struct Biotechnol J / Year: 2022
Title: Structural characterization of a cross-protective natural chimera of factor H binding protein from meningococcal serogroup B strain NL096.
Authors: Veggi, D. / Malito, E. / Lo Surdo, P. / Pansegrau, W. / Rippa, V. / Wahome, N. / Savino, S. / Masignani, V. / Pizza, M. / Bottomley, M.J.
#1: Journal: Patent / Year: 2020
Title: Neisseria meningitidis compositions and methods thereof
Authors: Jansen, K.U. / Anderson, A.S. / Absalon, J. / Aste-Amezaga, J.M. / Beeslaar, J.F. / Cooper, D. / Farley, J.E. / Fletcher, L.D. / Harris, S.L. / Jones, T.R. / Kanevsky, I. / Khandke, L. / ...Authors: Jansen, K.U. / Anderson, A.S. / Absalon, J. / Aste-Amezaga, J.M. / Beeslaar, J.F. / Cooper, D. / Farley, J.E. / Fletcher, L.D. / Harris, S.L. / Jones, T.R. / Kanevsky, I. / Khandke, L. / Liberator, P. / Perez, J.L. / Phelan, L.M. / Zlotnick, G.W.
History
DepositionMar 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Factor H binding protein variant 1-2,3.x
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0923
Polymers27,9001
Non-polymers1922
Water4,756264
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-14 kcal/mol
Surface area11900 Å2
Unit cell
Length a, b, c (Å)125.680, 42.610, 44.410
Angle α, β, γ (deg.)90.000, 100.200, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Factor H binding protein variant 1-2,3.x / Factor H binding protein variant A62_001 / Factor H binding protein variant A62_002


Mass: 27900.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: fhbp / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C0JF81
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.1 Å3/Da / Density % sol: 41.35 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1M tri-sodium citrate, 3.2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.219→23.37 Å / Num. obs: 65693 / % possible obs: 95.2 % / Redundancy: 3 % / Biso Wilson estimate: 10.1827524357 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 10.5
Reflection shellResolution: 1.22→1.264 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 9280

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PHENIX1.10_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KVD

3kvd


Resolution: 1.21998357323→23.3683816098 Å / SU ML: 0.0836274587195 / Cross valid method: FREE R-VALUE / σ(F): 1.3571381526 / Phase error: 15.1064659749
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.165911504385 3315 5.04996648589 %
Rwork0.141822105155 62329 -
obs0.143044838589 65644 95.1983177435 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.576031317 Å2
Refinement stepCycle: LAST / Resolution: 1.21998357323→23.3683816098 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1817 0 10 264 2091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01120101094831939
X-RAY DIFFRACTIONf_angle_d1.156915051162621
X-RAY DIFFRACTIONf_chiral_restr0.0971800465012292
X-RAY DIFFRACTIONf_plane_restr0.00710912870033345
X-RAY DIFFRACTIONf_dihedral_angle_d12.6975346417739
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.23740.192595162611200.1640855721332495X-RAY DIFFRACTION91.9479606188
1.2374-1.25590.1621593432441460.1560242467382515X-RAY DIFFRACTION92.0124481328
1.2559-1.27550.2003210430491340.1509754653892474X-RAY DIFFRACTION92.1554770318
1.2755-1.29640.1690537204141330.1458353291872535X-RAY DIFFRACTION92.9940745904
1.2964-1.31880.210263198421450.1445053985792506X-RAY DIFFRACTION93.5426958363
1.3188-1.34270.1894748744471460.1408924539182568X-RAY DIFFRACTION94.1380506417
1.3427-1.36860.1586481316671090.1391746178452534X-RAY DIFFRACTION93.3262711864
1.3686-1.39650.1720653247361210.1346231877462508X-RAY DIFFRACTION91.475295755
1.3965-1.42690.1636547248481580.131837145012548X-RAY DIFFRACTION95.0140449438
1.4269-1.460.1733598586151450.1254866338242578X-RAY DIFFRACTION95.2764170749
1.46-1.49660.1677858357391430.1302329813122603X-RAY DIFFRACTION96.1148057403
1.4966-1.5370.1521235426191510.1221697368782613X-RAY DIFFRACTION95.7063711911
1.537-1.58220.1417058654841290.1224230089432626X-RAY DIFFRACTION96.0264900662
1.5822-1.63330.1460672484741280.1227467557122623X-RAY DIFFRACTION96.2898144907
1.6333-1.69160.1611014019391340.1290169786082562X-RAY DIFFRACTION94.7960618847
1.6916-1.75940.1708827618721720.1315075244042609X-RAY DIFFRACTION96.4285714286
1.7594-1.83940.1692732817291130.1350346987372586X-RAY DIFFRACTION94.2388268156
1.8394-1.93630.1720330636621230.1343560479192623X-RAY DIFFRACTION94.6896551724
1.9363-2.05760.1373396467511420.1236789632642660X-RAY DIFFRACTION98.4193888303
2.0576-2.21630.1551965826651630.126560305292675X-RAY DIFFRACTION98.2686980609
2.2163-2.43920.1604702658821200.1412172186152703X-RAY DIFFRACTION98.0548801667
2.4392-2.79160.1632828936451440.1530238394672685X-RAY DIFFRACTION97.2164948454
2.7916-3.51520.1728381384841580.1582185873062674X-RAY DIFFRACTION96.9863013699
3.5152-23.3680.1744252987291380.1579604363992826X-RAY DIFFRACTION99.4964753273

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