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- PDB-6rcs: PfRH5-binding monoclonal antibody R5.016 -

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Basic information

Entry
Database: PDB / ID: 6rcs
TitlePfRH5-binding monoclonal antibody R5.016
Components
  • R5.016 heavy chain
  • R5.016 light chain
KeywordsIMMUNE SYSTEM / Plasmodium falciparum Erythrocyte invasion Neutralising antibody Human monoclonal antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAlanine, D.W.G. / Jamwal, A. / 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 1.2Aug 21, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: R5.016 heavy chain
B: R5.016 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0715
Polymers74,8572
Non-polymers2143
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-46 kcal/mol
Surface area20500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.080, 80.080, 162.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody R5.016 heavy chain


Mass: 50902.977 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 R5.016 light chain


Mass: 23953.613 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.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulfate, 0.1 M NaAc pH 4.5, 50% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.1→57.07 Å / Num. obs: 31807 / % possible obs: 100 % / Redundancy: 12.5 % / Biso Wilson estimate: 45.56 Å2 / Net I/σ(I): 16.4
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 1564

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→15.24 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.944 / SU R Cruickshank DPI: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.195 / SU Rfree Blow DPI: 0.156 / SU Rfree Cruickshank DPI: 0.154
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1579 4.99 %RANDOM
Rwork0.204 ---
obs0.205 31616 100 %-
Displacement parametersBiso mean: 52.52 Å2
Baniso -1Baniso -2Baniso -3
1-2.1473 Å20 Å20 Å2
2--2.1473 Å20 Å2
3----4.2947 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: 1 / Resolution: 2.1→15.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3222 0 13 187 3422
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013305HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.14491HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1083SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes549HARMONIC5
X-RAY DIFFRACTIONt_it3305HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.66
X-RAY DIFFRACTIONt_other_torsion18.07
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion439SEMIHARMONIC5
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_contact3353SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.17 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2308 157 5.48 %
Rwork0.2189 2708 -
all0.2196 2865 -
obs--99.86 %
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)
11.30420.27630.92561.2349-0.09791.32170-0.06050.04030.29360.0087-0.0316-0.2312-0.1003-0.0086-0.026-0.01740.0063-0.1462-0.0078-0.122862.652710.730986.1582
20.4881-0.23330.53360.5994-0.45421.88090.0479-0.0241-0.075-0.00460.02810.0395-0.0663-0.0057-0.076-0.0966-0.01190.0034-0.07310.0354-0.038860.5162-7.331584.9539
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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