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- PDB-6wla: Antigen binding fragment of ch128.1 -

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Basic information

Entry
Database: PDB / ID: 6wla
TitleAntigen binding fragment of ch128.1
Components
  • Fab ch128.1 heavy chain
  • Fab ch128.1 light chain
KeywordsIMMUNE SYSTEM / Antibody / Anti-huTfR1
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHelguera, G. / Rodriguez, J.A. / Sawaya, M. / Cascio, D. / Zink, S. / Ziegenbein, J. / Short, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R21AI135851-02 United States
CitationJournal: Nat Commun / Year: 2022
Title: Host receptor-targeted therapeutic approach to counter pathogenic New World mammarenavirus infections.
Authors: Hickerson, B.T. / Daniels-Wells, T.R. / Payes, C. / Clark, L.E. / Candelaria, P.V. / Bailey, K.W. / Sefing, E.J. / Zink, S. / Ziegenbein, J. / Abraham, J. / Helguera, G. / Penichet, M.L. / Gowen, B.B.
History
DepositionApr 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 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

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Assembly

Deposited unit
H1: Fab ch128.1 heavy chain
L1: Fab ch128.1 light chain
H2: Fab ch128.1 heavy chain
H3: Fab ch128.1 heavy chain
L3: Fab ch128.1 light chain
L2: Fab ch128.1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,14515
Polymers140,3166
Non-polymers8299
Water2,198122
1
H1: Fab ch128.1 heavy chain
L1: Fab ch128.1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1406
Polymers46,7722
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-21 kcal/mol
Surface area19050 Å2
MethodPISA
2
H2: Fab ch128.1 heavy chain
L2: Fab ch128.1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0485
Polymers46,7722
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-17 kcal/mol
Surface area19510 Å2
MethodPISA
3
H3: Fab ch128.1 heavy chain
L3: Fab ch128.1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9564
Polymers46,7722
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-19 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.270, 126.270, 94.850
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Antibody Fab ch128.1 heavy chain


Mass: 23495.211 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Fab ch128.1 light chain


Mass: 23276.797 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 3.11 Å3/Da / Density % sol: 60.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 1M Lithium chloride, 0.1 Citric acid pH 4.0, 20% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→63.13 Å / Num. obs: 51879 / % possible obs: 99.6 % / Redundancy: 5.294 % / Biso Wilson estimate: 55.576 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.129 / Rrim(I) all: 0.143 / Χ2: 1.047 / Net I/σ(I): 11.31 / Num. measured all: 274668
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.6-2.675.2791.2771.519935384737760.5391.41698.2
2.67-2.745.5071.0491.9420999381638130.6751.15999.9
2.74-2.825.4410.862.3219757363636310.7410.95299.9
2.82-2.915.370.6892.9619006354535390.8170.76499.8
2.91-35.2440.5493.6718050344334420.8690.611100
3-3.115.3580.4244.8717602329032850.9220.47199.8
3.11-3.225.3130.3276.2217282325832530.9580.36399.8
3.22-3.365.2050.257.8815933307230610.9710.27899.6
3.36-3.55.0540.1889.8415080299329840.980.2199.7
3.5-3.684.5730.1412.0912507277227350.9850.15998.7
3.68-3.875.3580.12215.0214317267826720.9920.13699.8
3.87-4.115.5560.09718.5314328258225790.9940.10799.9
4.11-4.395.4630.07522.3913045238923880.9950.083100
4.39-4.755.3920.06624.8912061223922370.9960.07399.9
4.75-5.25.3160.06624.6610765202920250.9970.07499.8
5.2-5.815.380.06823.619974185618540.9960.07599.9
5.81-6.715.0910.06522.048252162216210.9960.07399.9
6.71-8.225.0570.05325.566746137813340.9970.05996.8
8.22-11.625.5330.03635.515904106910670.9990.0499.8
11.62-63.135.360.03435.9931255845830.9990.03899.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_3724refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: fixed/fixed.pdb

Resolution: 2.6→63.13 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 27.75
RfactorNum. reflection% reflection
Rfree0.2581 5185 10 %
Rwork0.2072 --
obs0.2124 51861 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.84 Å2 / Biso mean: 57.8753 Å2 / Biso min: 24.12 Å2
Refinement stepCycle: final / Resolution: 2.6→63.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9848 0 54 122 10024
Biso mean--59.33 53.6 -
Num. residues----1290
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.630.32511700.28281525169596
2.63-2.660.32151720.26915511723100
2.66-2.690.36951720.265815511723100
2.69-2.730.32671730.261215571730100
2.73-2.760.33541740.276615721746100
2.76-2.80.35691710.274215381709100
2.8-2.840.31491730.278315621735100
2.84-2.880.35181780.255216061784100
2.88-2.930.33881720.246815451717100
2.93-2.980.30081730.242315561729100
2.98-3.030.34471730.225115611734100
3.03-3.080.311760.232415831759100
3.08-3.140.31861700.230915261696100
3.14-3.20.27861740.221715691743100
3.21-3.270.26241750.222715721747100
3.27-3.350.30831690.223215281697100
3.35-3.430.29091730.231915561729100
3.44-3.530.24911740.204115641738100
3.53-3.630.241700.20851524169498
3.63-3.750.271750.191215821757100
3.75-3.880.24691710.204215371708100
3.88-4.040.25771750.198615731748100
4.04-4.220.27311750.199315731748100
4.22-4.440.23261700.182915341704100
4.44-4.720.22071730.176615601733100
4.72-5.090.22331760.184215811757100
5.09-5.60.23391720.197615491721100
5.6-6.410.23221740.198715641738100
6.41-8.070.22391680.20441517168598
8.08-63.130.17421740.164415601734100

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