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- PDB-5ur8: Human antibody fragment (Fab) to meningococcal Factor H binding p... -

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Basic information

Entry
Database: PDB / ID: 5ur8
TitleHuman antibody fragment (Fab) to meningococcal Factor H binding protein
Components
  • human immunoglobulin gamma, heavy chain Fd fragment
  • human immunoglobulin gamma, kappa light chain
KeywordsIMMUNE SYSTEM / immunoglobulin gamma / fragment antigen binding / Fab / Factor H binding protein
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75500231418 Å
AuthorsBeernink, P.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI099125 United States
CitationJournal: Nat Commun / Year: 2018
Title: Crystal structure reveals vaccine elicited bactericidal human antibody targeting a conserved epitope on meningococcal fHbp.
Authors: Lopez-Sagaseta, J. / Beernink, P.T. / Bianchi, F. / Santini, L. / Frigimelica, E. / Lucas, A.H. / Pizza, M. / Bottomley, M.J.
History
DepositionFeb 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: human immunoglobulin gamma, heavy chain Fd fragment
B: human immunoglobulin gamma, kappa light chain


Theoretical massNumber of molelcules
Total (without water)49,1322
Polymers49,1322
Non-polymers00
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-29 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.900, 131.900, 90.381
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Antibody human immunoglobulin gamma, heavy chain Fd fragment


Mass: 25461.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Antibody human immunoglobulin gamma, kappa light chain


Mass: 23670.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 4.7 Å3/Da / Density % sol: 72.9 % / Description: rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 57.5% Tacsimate / Temp details: ambient temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2014
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.755→70.9 Å / Num. obs: 89767 / % possible obs: 97.4 % / Redundancy: 11.2 % / Biso Wilson estimate: 16.37 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.07 / Rsym value: 0.17 / Net I/av σ(I): 4.5 / Net I/σ(I): 12.6
Reflection shellResolution: 1.755→1.79 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 0.9 / CC1/2: 0.247 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Coot0.8.2model building
iMOSFLM7.2.1data reduction
SCALA3.3.21data scaling
PHASER1.10.1_2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LMJ

3lmj


Resolution: 1.75500231418→70.8777770677 Å / SU ML: 0.219706710888 / Cross valid method: FREE R-VALUE / σ(F): 1.3379225322 / Phase error: 22.3912513955
RfactorNum. reflection% reflectionSelection details
Rfree0.221736586333 4327 4.92583358947 %Random selection
Rwork0.198187247617 ---
obs0.199304846731 87843 97.0158484731 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27.6235107138 Å2
Refinement stepCycle: LAST / Resolution: 1.75500231418→70.8777770677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3383 0 0 312 3695
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006461567890843611
X-RAY DIFFRACTIONf_angle_d0.9082829750394958
X-RAY DIFFRACTIONf_chiral_restr0.0558312958483566
X-RAY DIFFRACTIONf_plane_restr0.00512615569671628
X-RAY DIFFRACTIONf_dihedral_angle_d13.98842337722237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.755-1.77490.3470689696551350.3289689599712494X-RAY DIFFRACTION88.2214765101
1.7749-1.79580.3091382879831370.3246608991912680X-RAY DIFFRACTION94.6890756303
1.7958-1.81770.3348851201551640.3086000304282719X-RAY DIFFRACTION96.035976016
1.8177-1.84070.3039121018691620.2987833972562663X-RAY DIFFRACTION94.7986577181
1.8407-1.8650.3019904150411460.2811163362822747X-RAY DIFFRACTION97.0154258887
1.865-1.89050.3170316466271420.2897722213572729X-RAY DIFFRACTION95.1607557176
1.8905-1.91750.2919259902011100.2695883579262760X-RAY DIFFRACTION96.2764173096
1.9175-1.94610.2923799457081370.2658184483392797X-RAY DIFFRACTION97.3457199735
1.9461-1.97660.3023288288591430.2501970944472680X-RAY DIFFRACTION94.7633434038
1.9766-2.0090.239475101851530.2367701359562739X-RAY DIFFRACTION96.6900702106
2.009-2.04360.2830953556231470.2315720166562784X-RAY DIFFRACTION97.63491006
2.0436-2.08080.242069720771380.2336732980962768X-RAY DIFFRACTION97.0283806344
2.0808-2.12080.2638477218251400.2217285359462757X-RAY DIFFRACTION96.7925158704
2.1208-2.16410.2450299999661500.2141845920872800X-RAY DIFFRACTION97.4884335757
2.1641-2.21120.2328525260451360.2113026294822780X-RAY DIFFRACTION97.5903614458
2.2112-2.26260.2441207702471510.2092923702542794X-RAY DIFFRACTION97.3875661376
2.2626-2.31920.2263852710921450.2014684894212800X-RAY DIFFRACTION97.5488572375
2.3192-2.38190.2197766678131700.1997217891912755X-RAY DIFFRACTION97.6953907816
2.3819-2.4520.2413724777581560.2161342084832788X-RAY DIFFRACTION98.1333333333
2.452-2.53110.2331077178481520.2082184012032806X-RAY DIFFRACTION98.239787446
2.5311-2.62160.2417383724161490.2097910894342817X-RAY DIFFRACTION98.309579052
2.6216-2.72660.2521403073541680.2154704212162788X-RAY DIFFRACTION97.7836586173
2.7266-2.85070.2296501523541380.216889687042825X-RAY DIFFRACTION98.3731739708
2.8507-3.00090.2388580346141370.2129052924322861X-RAY DIFFRACTION98.4241628365
3.0009-3.1890.2221803268021220.2046772690592860X-RAY DIFFRACTION98.8726790451
3.189-3.43520.2168246013151650.1873814970762837X-RAY DIFFRACTION98.6526454157
3.4352-3.78090.1986796613471590.1646603781622870X-RAY DIFFRACTION98.6323673071
3.7809-4.32790.1542059671781170.143487727482913X-RAY DIFFRACTION99.0519777705
4.3279-5.45240.1321216976651310.1285517733352864X-RAY DIFFRACTION96.8628719276
5.4524-70.93560.1643297453771270.1644889467613041X-RAY DIFFRACTION99.0928995934

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