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- PDB-4u0r: Plasmodium falciparum reticulocyte-binding protein homologue 5 (P... -

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Basic information

Entry
Database: PDB / ID: 4u0r
TitlePlasmodium falciparum reticulocyte-binding protein homologue 5 (PfRH5) bound to monoclonal antibody 9AD4
Components
  • Monoclonal antibody 9AD4 heavy chain
  • Monoclonal antibody 9AD4 light chain
  • Reticulocyte binding protein 5
KeywordsIMMUNE SYSTEM / malaria erythrocyte invasion antibody-mediated inhibition
Function / homologyRh5 coiled-coil domain / Rh5 coiled-coil domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Reticulocyte binding protein 5
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWright, K.E. / Hjerrild, K.A. / Bartlett, J. / Douglas, A.D. / Jin, J. / Brown, R.E. / Ashfield, R. / Clemmensen, S.B. / de Jongh, W.A. / Draper, S.J. / Higgins, M.K.
CitationJournal: Nature / Year: 2014
Title: Structure of malaria invasion protein RH5 with erythrocyte basigin and blocking antibodies.
Authors: Wright, K.E. / Hjerrild, K.A. / Bartlett, J. / Douglas, A.D. / Jin, J. / Brown, R.E. / Illingworth, J.J. / Ashfield, R. / Clemmensen, S.B. / de Jongh, W.A. / Draper, S.J. / Higgins, M.K.
History
DepositionJul 14, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Structure summary
Revision 1.2Aug 27, 2014Group: Database references
Revision 1.3Dec 3, 2014Group: Database references
Revision 1.4Jul 22, 2015Group: Source and taxonomy
Revision 1.5Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Reticulocyte binding protein 5
B: Monoclonal antibody 9AD4 heavy chain
C: Monoclonal antibody 9AD4 light chain


Theoretical massNumber of molelcules
Total (without water)117,0293
Polymers117,0293
Non-polymers00
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-33 kcal/mol
Surface area33700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.790, 86.660, 324.040
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: Protein Reticulocyte binding protein 5 / reticulocyte-binding protein homologue 5 / PfRH5


Mass: 63128.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Drosophila melanogaster (fruit fly) / References: UniProt: B2L3N7
#2: Antibody Monoclonal antibody 9AD4 heavy chain


Mass: 27641.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Oryctolagus cuniculus (rabbit)
#3: Antibody Monoclonal antibody 9AD4 light chain


Mass: 26259.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Oryctolagus cuniculus (rabbit)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 24% PEG 1500, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.3→41.86 Å / Num. obs: 49434 / % possible obs: 96.2 % / Redundancy: 5 % / Biso Wilson estimate: 48.97 Å2 / Net I/σ(I): 9.8
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 2 / % possible all: 83.3

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QQ9, 3HR5

3qq9

3hr5


Resolution: 2.3→40.83 Å / Cor.coef. Fo:Fc: 0.9086 / Cor.coef. Fo:Fc free: 0.8801 / SU R Cruickshank DPI: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.236 / SU Rfree Blow DPI: 0.202 / SU Rfree Cruickshank DPI: 0.206
RfactorNum. reflection% reflectionSelection details
Rfree0.2583 2462 4.99 %RANDOM
Rwork0.221 ---
obs0.2229 49336 96.09 %-
Displacement parametersBiso mean: 54.18 Å2
Baniso -1Baniso -2Baniso -3
1-8.2249 Å20 Å20 Å2
2---18.2177 Å20 Å2
3---9.9928 Å2
Refine analyzeLuzzati coordinate error obs: 0.392 Å
Refinement stepCycle: 1 / Resolution: 2.3→40.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5784 0 0 210 5994
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015921HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.198013HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2044SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes136HARMONIC2
X-RAY DIFFRACTIONt_gen_planes845HARMONIC5
X-RAY DIFFRACTIONt_it5921HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.03
X-RAY DIFFRACTIONt_other_torsion21.45
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion792SEMIHARMONIC5
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_contact6443SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2593 134 4.49 %
Rwork0.2381 2850 -
all0.239 2984 -
obs--96.09 %
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)
11.92351.3324-1.80361.4788-2.05073.11220.11950.34520.09080.1604-0.07490.0042-0.51750.0022-0.0446-0.00190.03930.0022-0.00920.1352-0.21814.588795.0877351.998
20.1310.14710.30260.60690.92963.12950.08680.00640.0012-0.08380.1368-0.09320.03510.2804-0.2236-0.1428-0.00270-0.0177-0.0110.046711.864887.8813411.613
30.24410.1660.60671.01660.32620.9862-0.1304-0.03450.0989-0.2560.0416-0.0959-0.25560.23460.0888-0.0901-0.05550.0502-0.01140.0204-0.002913.3576105.278413.257
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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