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- PDB-5o1r: human Fab 5H2 bound to NHBA-C3 from Neisseria meningitidis serogroup B -

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Basic information

Entry
Database: PDB / ID: 5o1r
Titlehuman Fab 5H2 bound to NHBA-C3 from Neisseria meningitidis serogroup B
Components
  • GNA2132
  • IGH@ protein
  • Uncharacterized protein
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


cell outer membrane / heparin binding / cell adhesion / DNA binding / extracellular region / plasma membrane
Similarity search - Function
Transferrin-binding protein B, C-lobe/N-lobe beta barrel domain / C-lobe and N-lobe beta barrels of Tf-binding protein B / Porin - #90 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / : / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain ...Transferrin-binding protein B, C-lobe/N-lobe beta barrel domain / C-lobe and N-lobe beta barrels of Tf-binding protein B / Porin - #90 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / : / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig-like domain-containing protein / IGH@ protein / Neisserial heparin binding antigen
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsMalito, E. / Maritan, M.
CitationJournal: PLoS ONE / Year: 2018
Title: Structures of NHBA elucidate a broadly conserved epitope identified by a vaccine induced antibody.
Authors: Maritan, M. / Veggi, D. / Cozzi, R. / Dello Iacono, L. / Bartolini, E. / Lo Surdo, P. / Maruggi, G. / Spraggon, G. / Bottomley, M.J. / Malito, E.
History
DepositionMay 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.3Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Jan 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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GNA2132
B: GNA2132
H: IGH@ protein
I: IGH@ protein
L: Uncharacterized protein
M: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,83711
Polymers129,5276
Non-polymers3105
Water82946
1
A: GNA2132
H: IGH@ protein
L: Uncharacterized protein
hetero molecules


  • defined by author
  • Evidence: gel filtration, the complex was isolated by gel filtration chromatography showing an elution profile compatible with the complex. The fractions corresponding to the peak were also run in ...Evidence: gel filtration, the complex was isolated by gel filtration chromatography showing an elution profile compatible with the complex. The fractions corresponding to the peak were also run in SDS-PAGE under both native and denaturant conditions, showing the presence of both the Fab and NHBA-C3
  • 64.9 kDa, 3 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)64,8885
Polymers64,7643
Non-polymers1242
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GNA2132
I: IGH@ protein
M: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9506
Polymers64,7643
Non-polymers1863
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.450, 119.450, 364.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein GNA2132 / Gna2132 / Heparin binding protein / Neisserial heparin binding antigen / Putative lipoprotein GNA2132


Mass: 13706.022 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: gna2132, nhba / Variant: p20 / Plasmid: pET21b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): T1R / References: UniProt: Q9JPP1
#2: Antibody IGH@ protein


Mass: 27962.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: the sequence provided includes the tag which was cleaved prior to crystallization
Source: (gene. exp.) Homo sapiens (human) / Gene: IGH@ / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q6GMX6
#3: Antibody Uncharacterized protein


Mass: 23094.561 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q6GMX0
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
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: 2.9 Å3/Da / Density % sol: 57.52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M TRIS pH 8.0 and 1.6 M lithium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.86→91.05 Å / Num. obs: 36688 / % possible obs: 100 % / Redundancy: 19.4 % / Biso Wilson estimate: 88.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.044 / Rrim(I) all: 0.194 / Net I/σ(I): 18.4
Reflection shellResolution: 2.86→2.93 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 2628 / CC1/2: 0.557 / Rpim(I) all: 0.875 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NYX

5nyx


Resolution: 2.86→78.74 Å / Cor.coef. Fo:Fc: 0.9465 / Cor.coef. Fo:Fc free: 0.9196 / SU R Cruickshank DPI: 0.826 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.926 / SU Rfree Blow DPI: 0.301 / SU Rfree Cruickshank DPI: 0.303
RfactorNum. reflection% reflectionSelection details
Rfree0.2223 1775 4.85 %RANDOM
Rwork0.1778 ---
obs0.1799 36573 99.95 %-
Displacement parametersBiso mean: 84.55 Å2
Baniso -1Baniso -2Baniso -3
1--7.5165 Å20 Å20 Å2
2---7.5165 Å20 Å2
3---15.0329 Å2
Refine analyzeLuzzati coordinate error obs: 0.447 Å
Refinement stepCycle: 1 / Resolution: 2.86→78.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8260 0 20 46 8326
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018499HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2911543HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2808SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes167HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1251HARMONIC5
X-RAY DIFFRACTIONt_it8499HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.17
X-RAY DIFFRACTIONt_other_torsion21.47
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1108SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9131SEMIHARMONIC4
LS refinement shellResolution: 2.86→2.94 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2574 149 5.12 %
Rwork0.2523 2762 -
all0.2526 2911 -
obs--99.95 %
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)
16.18460.9618-0.70863.3406-0.434.5068-0.13160.2319-0.09740.12560.1619-0.04410.6718-0.1984-0.03030.0983-0.00520.0067-0.1081-0.0179-0.2994-13.533821.224833.9923
24.8081-1.5356-1.20753.17760.23583.8809-0.04210.1213-0.0397-0.0690.08770.10070.5668-0.3236-0.04560.0394-0.1424-0.0251-0.0593-0.0036-0.231320.957513.4777-10.0893
30.7081-0.09990.06061.9509-0.98442.4879-0.0223-0.01570.19460.21810.02070.0433-0.0382-0.10330.0016-0.19930.09150.02950.02680.0116-0.0851-6.071352.598310.9504
41.28840.29930.05052.21281.15663.1310.00850.04670.1525-0.05440.0255-0.12020.01190.1561-0.034-0.2513-0.01650.012-0.00550.0788-0.072527.778345.107312.8121
51.2860.1909-0.55532.7228-1.59063.6329-0.01140.22320.1332-0.33210.017-0.15630.3045-0.1268-0.0056-0.24230.09750.0160.04160.0332-0.2329-2.621343.6713-4.9052
61.29670.132-0.01962.36561.03643.4812-0.0186-0.14060.28480.3792-0.00490.0474-0.0608-0.04970.0236-0.19970.02520.0112-0.04570.0248-0.206520.601138.523128.8653
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|292 - A|407 }
2X-RAY DIFFRACTION2{ B|292 - B|406 }
3X-RAY DIFFRACTION3{ H|1 - H|223 }
4X-RAY DIFFRACTION4{ I|1 - I|223 }
5X-RAY DIFFRACTION5{ L|1 - L|211 }
6X-RAY DIFFRACTION6{ M|1 - M|211 }

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