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- PDB-8awl: Fab RVFV-268 -

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Basic information

Entry
Database: PDB / ID: 8awl
TitleFab RVFV-268
Components
  • Heavy chain Fab268
  • Light chain Fab268
KeywordsIMMUNE SYSTEM / Fab fragment antibody
Function / homologyCITRIC ACID
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.62 Å
AuthorsHulswit, R.J.G. / Bowden, T.A. / Stass, R.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust203141/Z/16/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/V031635/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/S007555/1 United Kingdom
CitationJournal: Nat Commun / Year: 2023
Title: Multifunctional human monoclonal antibody combination mediates protection against Rift Valley fever virus at low doses.
Authors: Chapman, N.S. / Hulswit, R.J.G. / Westover, J.L.B. / Stass, R. / Paesen, G.C. / Binshtein, E. / Reidy, J.X. / Engdahl, T.B. / Handal, L.S. / Flores, A. / Gowen, B.B. / Bowden, T.A. / Crowe Jr., J.E.
History
DepositionAug 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Heavy chain Fab268
L: Light chain Fab268
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5943
Polymers46,4022
Non-polymers1921
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-24 kcal/mol
Surface area19610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.382, 70.388, 129.942
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Heavy chain Fab268


Mass: 23633.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Light chain Fab268


Mass: 22768.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.68 Å3/Da / Density % sol: 54.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M citric acid pH 3.5, 20% w/v polyethylene glycol (PEG) 1,500 and 4% v/v (+/-)-2-methyl-2,4-pentanediol
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.62→47.74 Å / Num. obs: 64027 / % possible obs: 99.5 % / Redundancy: 13.3 % / CC1/2: 1 / Net I/σ(I): 11.4
Reflection shellResolution: 1.62→1.65 Å / Num. unique obs: 3003 / CC1/2: 0.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZMJ

5zmj


Resolution: 1.62→47.74 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2192 3086 4.84 %
Rwork0.2021 60640 -
obs0.203 63726 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.07 Å2 / Biso mean: 33.4045 Å2 / Biso min: 19.09 Å2
Refinement stepCycle: final / Resolution: 1.62→47.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3214 0 18 201 3433
Biso mean--87.81 35.63 -
Num. residues----425
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.62-1.640.47321180.44222419253788
1.64-1.670.4241150.41432679279498
1.67-1.70.43141350.40012712284798
1.7-1.730.36261280.35827412869100
1.73-1.760.34121380.32342732287099
1.76-1.80.33031540.278627292883100
1.8-1.840.2861450.24992695284099
1.84-1.880.24221560.2192746290299
1.88-1.930.25791250.208327602885100
1.93-1.980.22821390.210127442883100
1.98-2.040.24271500.217827472897100
2.04-2.110.25991440.229427642908100
2.11-2.180.2631260.212927862912100
2.18-2.270.24261690.204127502919100
2.27-2.370.23071330.220427652898100
2.37-2.50.27491340.223527932927100
2.5-2.650.25351400.222627872927100
2.65-2.860.24451370.219128272964100
2.86-3.140.22981440.215428022946100
3.15-3.60.21391520.186428232975100
3.6-4.530.15221470.156428623009100
4.54-47.740.16681570.16412977313499
Refinement TLS params.Method: refined / Origin x: -42.9439 Å / Origin y: -24.517 Å / Origin z: 16.5363 Å
111213212223313233
T0.2145 Å20.0079 Å20.0356 Å2-0.2128 Å2-0.0044 Å2--0.1895 Å2
L0.9335 °2-0.0013 °20.6633 °2-0.3794 °2-0.0058 °2--0.579 °2
S0.0331 Å °0.0088 Å °-0.0235 Å °0.0537 Å °0.0053 Å °0.0149 Å °0.0023 Å °-0.0359 Å °-0.038 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allH1 - 227
2X-RAY DIFFRACTION1allH301
3X-RAY DIFFRACTION1allL1 - 227
4X-RAY DIFFRACTION1allB1 - 201

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