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- PDB-6rcq: PfRH5-binding monoclonal antibody R5.011 -

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Basic information

Entry
Database: PDB / ID: 6rcq
TitlePfRH5-binding monoclonal antibody R5.011
Components
  • R5.011 heavy chain
  • R5.011 light chain
KeywordsIMMUNE SYSTEM / Plasmodium falciparum Erythrocyte invasion Potentiating antibody Human monoclonal antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION / CACODYLATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsAlanine, D.W.G. / Draper, S.J. / Higgins, M.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Cell / Year: 2019
Title: Human Antibodies that Slow Erythrocyte Invasion Potentiate Malaria-Neutralizing Antibodies.
Authors: Alanine, D.G.W. / Quinkert, D. / Kumarasingha, R. / Mehmood, S. / Donnellan, F.R. / Minkah, N.K. / Dadonaite, B. / Diouf, A. / Galaway, F. / Silk, S.E. / Jamwal, A. / Marshall, J.M. / Miura, ...Authors: Alanine, D.G.W. / Quinkert, D. / Kumarasingha, R. / Mehmood, S. / Donnellan, F.R. / Minkah, N.K. / Dadonaite, B. / Diouf, A. / Galaway, F. / Silk, S.E. / Jamwal, A. / Marshall, J.M. / Miura, K. / Foquet, L. / Elias, S.C. / Labbe, G.M. / Douglas, A.D. / Jin, J. / Payne, R.O. / Illingworth, J.J. / Pattinson, D.J. / Pulido, D. / Williams, B.G. / de Jongh, W.A. / Wright, G.J. / Kappe, S.H.I. / Robinson, C.V. / Long, C.A. / Crabb, B.S. / Gilson, P.R. / Higgins, M.K. / Draper, S.J.
History
DepositionApr 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev / database_PDB_rev_record
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: R5.011 heavy chain
B: R5.011 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9474
Polymers48,7512
Non-polymers1962
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-23 kcal/mol
Surface area19940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.858, 86.375, 127.409
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody R5.011 heavy chain


Mass: 25685.484 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 R5.011 light chain


Mass: 23065.367 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.7 Å3/Da / Density % sol: 54.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.16 M ZnAc, 0.108 M Na cacodylate pH 6.5, 14.4% PEG 8000, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.28→47.86 Å / Num. obs: 24770 / % possible obs: 99.3 % / Redundancy: 12.8 % / Biso Wilson estimate: 44.78 Å2 / Net I/σ(I): 11
Reflection shellResolution: 2.28→2.36 Å / Num. unique obs: 2284

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→44.8 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.26 / SU Rfree Blow DPI: 0.199 / SU Rfree Cruickshank DPI: 0.195
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1262 5.11 %RANDOM
Rwork0.185 ---
obs0.188 24709 99.5 %-
Displacement parametersBiso mean: 39.67 Å2
Baniso -1Baniso -2Baniso -3
1--9.5938 Å20 Å20 Å2
2--3.4493 Å20 Å2
3---6.1445 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: 1 / Resolution: 2.28→44.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3247 0 9 238 3494
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013341HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.234567HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1054SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes556HARMONIC5
X-RAY DIFFRACTIONt_it3341HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.8
X-RAY DIFFRACTIONt_other_torsion18.99
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion441SEMIHARMONIC5
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_contact3704SEMIHARMONIC4
LS refinement shellResolution: 2.28→2.38 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2411 143 5.02 %
Rwork0.2118 2708 -
all0.2134 2851 -
obs--96.24 %
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)
10.63920.26641.09640.49740.08782.1152-0.00620.0185-0.00060.0483-0.0363-0.0518-0.0084-0.02810.0425-0.11920.02420.0196-0.0612-0.0032-0.021314.65103.856140.899
20.16430.22140.49910.33370.13342.41990.04640.0371-0.04870.04240.05660.04950.15720.0226-0.103-0.04220.01630.0022-0.12620.0041-0.074316.50187.8637147.528
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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