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- PDB-7jz1: Crystal structure of broadly Plasmodium RIFIN reactive LAIR1-inse... -

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Basic information

Entry
Database: PDB / ID: 7jz1
TitleCrystal structure of broadly Plasmodium RIFIN reactive LAIR1-inserted antibody MGC34
Components
  • MGC34 heavy chain
  • MGC34 light chain
KeywordsIMMUNE SYSTEM / LAIR1 / insertion / antibody / RIFIN / Malaria
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.37 Å
AuthorsXu, K. / Kwong, P.D.
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis of LAIR1 targeting by polymorphic Plasmodium RIFINs.
Authors: Xu, K. / Wang, Y. / Shen, C.H. / Chen, Y. / Zhang, B. / Liu, K. / Tsybovsky, Y. / Wang, S. / Farney, S.K. / Gorman, J. / Stephens, T. / Verardi, R. / Yang, Y. / Zhou, T. / Chuang, G.Y. / ...Authors: Xu, K. / Wang, Y. / Shen, C.H. / Chen, Y. / Zhang, B. / Liu, K. / Tsybovsky, Y. / Wang, S. / Farney, S.K. / Gorman, J. / Stephens, T. / Verardi, R. / Yang, Y. / Zhou, T. / Chuang, G.Y. / Lanzavecchia, A. / Piccoli, L. / Kwong, P.D.
History
DepositionSep 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: 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 1.2Oct 18, 2023Group: 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
H: MGC34 heavy chain
L: MGC34 light chain


Theoretical massNumber of molelcules
Total (without water)61,9892
Polymers61,9892
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-36 kcal/mol
Surface area26320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.379, 101.379, 319.878
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Antibody MGC34 heavy chain


Mass: 38874.250 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 MGC34 light chain


Mass: 23114.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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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: 3.83 Å3/Da / Density % sol: 67.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MgCl2 hexahydrate, 0.1 M Tris HCl pH 8.5, 20% PEG 3350, 25% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. obs: 14664 / % possible obs: 99.8 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.094 / Rrim(I) all: 0.202 / Χ2: 1.328 / Net I/σ(I): 3.7 / Num. measured all: 62324
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.35-3.473.70.78414160.6030.4450.9090.627100
3.47-3.6140.63414260.7530.3430.7250.676100
3.61-3.774.30.54514030.7580.2880.620.712100
3.77-3.974.40.38814400.8940.2040.4410.848100
3.97-4.224.50.30114380.9220.1550.3411.048100
4.22-4.554.50.22214370.9510.1150.2521.60799.7
4.55-54.50.1914550.9630.0990.2151.74799.7
5-5.734.40.1614740.9670.0820.1811.656100
5.73-7.214.40.13215290.980.0690.151.58699.9
7.21-503.90.09716460.9880.0550.1122.51199.1

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KGR

3kgr


Resolution: 3.37→42.33 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2548 691 4.74 %
Rwork0.2383 13894 -
obs0.2391 14585 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 245.35 Å2 / Biso mean: 107.8429 Å2 / Biso min: 61.4 Å2
Refinement stepCycle: final / Resolution: 3.37→42.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4276 0 0 0 4276
Num. residues----564
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.37-3.630.33081250.310427152840
3.63-3.990.28971270.290327022829
3.99-4.570.26341320.225527342866
4.57-5.750.24091550.222727572912
5.75-42.330.23481520.221829863138

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