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- PDB-4qex: Crystal structure of PfEBA-175 RII in complex with a Fab fragment... -

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Basic information

Entry
Database: PDB / ID: 4qex
TitleCrystal structure of PfEBA-175 RII in complex with a Fab fragment from inhibitory antibody R217
Components
  • Antibody Heavy Chain
  • Antibody Light Chain
  • Erythrocyte-binding antigen-175
KeywordsIMMUNE SYSTEM / Duffy Binding Like (DBL) domain / Immunoglobulin domain / Invasion / adhesion / immunity / PFEBA-175 / Antibody / Cell Surface / Extrecellular / Cell Adhesion / Receptor / Ligand
Function / homologyErythrocyte binding antigen 175, C-terminal / Erythrocyte binding antigen 175, C-terminal domain superfamily / Erythrocyte binding antigen 175 / Duffy-antigen binding / Duffy-antigen binding superfamily / Duffy binding domain / host cell surface receptor binding / membrane / Erythrocyte-binding antigen-175
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å
AuthorsChen, E. / Paing, M.M. / Salinas, N. / Sim, B.K. / Tolia, N.H.
CitationJournal: Plos Pathog. / Year: 2013
Title: Structural and Functional Basis for Inhibition of Erythrocyte Invasion by Antibodies that Target Plasmodium falciparum EBA-175.
Authors: Chen, E. / Paing, M.M. / Salinas, N. / Sim, B.K. / Tolia, N.H.
History
DepositionMay 19, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionJun 4, 2014ID: 4K4M
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Erythrocyte-binding antigen-175
L: Antibody Light Chain
H: Antibody Heavy Chain
B: Erythrocyte-binding antigen-175
M: Antibody Light Chain
I: Antibody Heavy Chain


Theoretical massNumber of molelcules
Total (without water)237,4106
Polymers237,4106
Non-polymers00
Water00
1
A: Erythrocyte-binding antigen-175
L: Antibody Light Chain
H: Antibody Heavy Chain


Theoretical massNumber of molelcules
Total (without water)118,7053
Polymers118,7053
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Erythrocyte-binding antigen-175
M: Antibody Light Chain
I: Antibody Heavy Chain


Theoretical massNumber of molelcules
Total (without water)118,7053
Polymers118,7053
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)208.100, 101.260, 117.590
Angle α, β, γ (deg.)90.00, 102.86, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'B' and (resseq 8:55 or resseq 57:508 or resseq 517:596 ) and (not element H)
211chain 'A' and (resseq 17:49 or resseq 57:129 or resseq...
112chain 'I' and (resseq 2:52 or resseq 52:82 or resseq...
212chain 'H' and (resseq 2:52 or resseq 52:82 or resseq...
113chain 'M' and (resseq 1:30 or resseq 30:30 or resseq...
213chain 'L' and (resseq 1:30 or resseq 30:30 or resseq...

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Erythrocyte-binding antigen-175


Mass: 72184.391 Da / Num. of mol.: 2 / Mutation: N3Q, S50A, S195A, T206A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: EBA-175 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q05644
#2: Antibody Antibody Light Chain


Mass: 23622.992 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody Antibody Heavy Chain


Mass: 22897.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
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: 2.54 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.3 M magnesium chloride, 8% benzamidine hydrochloride, 7.5% glycerol, 18% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 3, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 4.5→20 Å / Num. all: 14361 / Num. obs: 13322 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 4.5→4.6 Å / % possible all: 52.8

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.5→19.842 Å / SU ML: 0.63 / σ(F): 1.99 / Phase error: 31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2855 666 5 %RANDOM
Rwork0.2321 ---
obs0.2348 13315 93.97 %-
all-14361 --
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.5→19.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16029 0 0 0 16029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00316420
X-RAY DIFFRACTIONf_angle_d0.66522102
X-RAY DIFFRACTIONf_dihedral_angle_d12.7726164
X-RAY DIFFRACTIONf_chiral_restr0.0442349
X-RAY DIFFRACTIONf_plane_restr0.0032819
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B4734X-RAY DIFFRACTIONPOSITIONAL
12A4734X-RAY DIFFRACTIONPOSITIONAL0.015
21I1548X-RAY DIFFRACTIONPOSITIONAL
22H1548X-RAY DIFFRACTIONPOSITIONAL0.021
31M1645X-RAY DIFFRACTIONPOSITIONAL
32L1645X-RAY DIFFRACTIONPOSITIONAL0.008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.5002-4.8430.29951040.28311983X-RAY DIFFRACTION74
4.843-5.32190.3541390.26882648X-RAY DIFFRACTION99
5.3219-6.07260.30461400.26332649X-RAY DIFFRACTION99
6.0726-7.57920.3231400.24092654X-RAY DIFFRACTION99
7.5792-19.84170.22831430.18432715X-RAY DIFFRACTION99

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