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- PDB-8up2: Murine Fab JAR 4 bound to meningococcal Factor H binding protein -

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Basic information

Entry
Database: PDB / ID: 8up2
TitleMurine Fab JAR 4 bound to meningococcal Factor H binding protein
Components
  • (Human-mouse chimeric ...) x 2
  • Factor H binding protein, sequence variant ID 1
KeywordsIMMUNE SYSTEM / Antibody / Fab / antigen / Factor H binding protein
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 / ACETATE ION / Factor H binding protein variant B24
Function and homology information
Biological speciesMus musculus (house mouse)
Neisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBeernink, P.T. / Beernink, B.P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of murine Fab JAR 4 bound to FHbp at 1.60-Angstroms resolution
Authors: Beernink, P.T. / Beernink, B.P.
History
DepositionOct 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Human-mouse chimeric immunoglobulin heavy chain, Fd fragment
B: Human-mouse chimeric immunoglobulin, kappa light chain
C: Factor H binding protein, sequence variant ID 1
D: Human-mouse chimeric immunoglobulin heavy chain, Fd fragment
E: Human-mouse chimeric immunoglobulin, kappa light chain
F: Factor H binding protein, sequence variant ID 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,8819
Polymers151,6386
Non-polymers2433
Water18,2851015
1
A: Human-mouse chimeric immunoglobulin heavy chain, Fd fragment
B: Human-mouse chimeric immunoglobulin, kappa light chain
C: Factor H binding protein, sequence variant ID 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9114
Polymers75,8193
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Human-mouse chimeric immunoglobulin heavy chain, Fd fragment
E: Human-mouse chimeric immunoglobulin, kappa light chain
F: Factor H binding protein, sequence variant ID 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9705
Polymers75,8193
Non-polymers1512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.430, 67.440, 168.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 9 or resid 11 through 53 or resid 55 through 218))
d_2ens_1(chain "D" and (resid 1 through 9 or resid 11 through 53 or resid 55 through 218))
d_1ens_2(chain "B" and resid 1 through 216)
d_2ens_2chain "E"
d_1ens_3(chain "C" and (resid 14 through 32 or resid 34 through 256 or resid 302))
d_2ens_3(chain "F" and (resid 14 through 32 or resid 34 through 301))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLUGLUPROPROAA1 - 91 - 9
d_12ens_1LEULEUPROPROAA11 - 5311 - 53
d_13ens_1ASNASNPROPROAA55 - 21855 - 218
d_21ens_1GLUGLUPROPRODD1 - 91 - 9
d_22ens_1LEULEUPROPRODD11 - 5311 - 53
d_23ens_1ASNASNPROPRODD55 - 21855 - 218
d_11ens_2ASPASPARGARGBB1 - 2161 - 216
d_21ens_2ASPASPARGARGEE1 - 2161 - 216
d_11ens_3ALAALAGLNGLNCC14 - 328 - 26
d_12ens_3LEULEULEULEUCC34 - 25628 - 250
d_13ens_3GOLGOLGOLGOLCG302
d_21ens_3ALAALAGLNGLNFF14 - 328 - 26
d_22ens_3LEULEULEULEUFF34 - 25628 - 250
d_23ens_3GOLGOLGOLGOLFI301

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.999972397177, -0.000239542298023, -0.00742613645824), (-0.000225135398061, -0.9999980913, 0.00194080154615), (-0.00742658718803, -0.00193907608836, -0.999970542459)-0.0125604018591, -14.2433754306, 84.463094337
2given(0.99998148635, 0.00197313284541, -0.0057561882448), (0.00197973540258, -0.999997388736, 0.00114156402349), (-0.00575392075641, -0.00115293861863, -0.999982781416)-0.0152358762602, -14.2900032264, 84.3652487847
3given(0.99997466645, 0.000273122430945, 0.0071127956132), (0.000283724143959, -0.999998850375, -0.00148954642283), (0.00711238060761, 0.00149152675918, -0.999973594346)-0.323402738513, -14.2490135654, 83.8508725439

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Components

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Protein , 1 types, 2 molecules CF

#3: Protein Factor H binding protein, sequence variant ID 1


Mass: 27699.939 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: fhbp / Production host: Escherichia coli (E. coli) / References: UniProt: Q6VRZ6

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Antibody , 2 types, 4 molecules ADBE

#1: Antibody Human-mouse chimeric immunoglobulin heavy chain, Fd fragment


Mass: 23920.861 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Human-mouse chimeric immunoglobulin, kappa light chain


Mass: 24198.158 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 3 types, 1018 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1015 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.79 Å3/Da / Density % sol: 55.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.05M NaOAc 20% PEG 4,000 0.085M Tris Cl, pH 8.5 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 1.6→74.43 Å / Num. obs: 218509 / % possible obs: 99.9 % / Redundancy: 9.4 % / Biso Wilson estimate: 19.87 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.1642 / Rpim(I) all: 0.0698 / Net I/av σ(I): 5.84 / Net I/σ(I): 5.84
Reflection shellResolution: 1.603→1.66 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.366 / Mean I/σ(I) obs: 1.32 / Num. unique obs: 133437 / CC1/2: 0.489 / Rpim(I) all: 0.5865 / % possible all: 99.53

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→74.43 Å / SU ML: 0.1716 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.4181
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.212 2014 0.92 %
Rwork0.1874 216438 -
obs0.1877 218452 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.87 Å2
Refinement stepCycle: LAST / Resolution: 1.6→74.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10164 0 16 1015 11195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010510396
X-RAY DIFFRACTIONf_angle_d1.102114069
X-RAY DIFFRACTIONf_chiral_restr0.06381576
X-RAY DIFFRACTIONf_plane_restr0.01861805
X-RAY DIFFRACTIONf_dihedral_angle_d14.85983776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.29681430.265315417X-RAY DIFFRACTION99.42
1.64-1.690.26951390.238415390X-RAY DIFFRACTION99.81
1.69-1.740.27321430.237215359X-RAY DIFFRACTION99.8
1.74-1.790.27691440.230215380X-RAY DIFFRACTION99.78
1.79-1.860.33851410.238215435X-RAY DIFFRACTION99.77
1.86-1.930.29051430.207115369X-RAY DIFFRACTION99.78
1.93-2.020.20481430.199715388X-RAY DIFFRACTION99.74
2.02-2.130.22381480.189915408X-RAY DIFFRACTION99.78
2.13-2.260.25531410.197515440X-RAY DIFFRACTION99.69
2.26-2.430.25161440.188115412X-RAY DIFFRACTION99.81
2.43-2.680.23411430.197415521X-RAY DIFFRACTION99.83
2.68-3.070.24831440.184215533X-RAY DIFFRACTION99.9
3.07-3.860.1831470.172915575X-RAY DIFFRACTION99.84
3.86-74.430.14021510.155215811X-RAY DIFFRACTION99.67

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