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- PDB-7raj: Structure of PfCSP peptide 21 with antibody iGL-CIS43.D3 -

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Basic information

Entry
Database: PDB / ID: 7raj
TitleStructure of PfCSP peptide 21 with antibody iGL-CIS43.D3
Components
  • (iGL-CIS43.D3 Fab ...) x 2
  • ASN-PRO-ASP-PRO-ASN-ALA-ASN-PRO-ASN-VAL-ASP-PRO-ASN-ALA-ASN
KeywordsIMMUNE SYSTEM / Antibody / Plasmodium falciparum
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsTripathi, P. / Kwong, P.D.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
CitationJournal: Immunity / Year: 2021
Title: Vaccination in a humanized mouse model elicits highly protective PfCSP-targeting anti-malarial antibodies.
Authors: Kratochvil, S. / Shen, C.H. / Lin, Y.C. / Xu, K. / Nair, U. / Da Silva Pereira, L. / Tripathi, P. / Arnold, J. / Chuang, G.Y. / Melzi, E. / Schon, A. / Zhang, B. / Dillon, M. / Bonilla, B. / ...Authors: Kratochvil, S. / Shen, C.H. / Lin, Y.C. / Xu, K. / Nair, U. / Da Silva Pereira, L. / Tripathi, P. / Arnold, J. / Chuang, G.Y. / Melzi, E. / Schon, A. / Zhang, B. / Dillon, M. / Bonilla, B. / Flynn, B.J. / Kirsch, K.H. / Kisalu, N.K. / Kiyuka, P.K. / Liu, T. / Ou, L. / Pancera, M. / Rawi, R. / Reveiz, M. / Seignon, K. / Wang, L.T. / Waring, M.T. / Warner, J. / Yang, Y. / Francica, J.R. / Idris, A.H. / Seder, R.A. / Kwong, P.D. / Batista, F.D.
History
DepositionJul 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: iGL-CIS43.D3 Fab Heavy chain
L: iGL-CIS43.D3 Fab light chain
A: ASN-PRO-ASP-PRO-ASN-ALA-ASN-PRO-ASN-VAL-ASP-PRO-ASN-ALA-ASN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3826
Polymers50,0563
Non-polymers3263
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-90 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.281, 89.712, 72.044
Angle α, β, γ (deg.)90.000, 99.270, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein/peptide , 1 types, 1 molecules A

#3: Protein/peptide ASN-PRO-ASP-PRO-ASN-ALA-ASN-PRO-ASN-VAL-ASP-PRO-ASN-ALA-ASN


Mass: 1562.553 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)

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Antibody , 2 types, 2 molecules HL

#1: Antibody iGL-CIS43.D3 Fab Heavy chain


Mass: 24245.312 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 iGL-CIS43.D3 Fab light chain


Mass: 24247.854 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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Non-polymers , 3 types, 5 molecules

#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.2 M Zn acetate, 0.1 M MES, 17.53% w/v PEG 8000

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→36.79 Å / Num. obs: 9207 / % possible obs: 97.19 % / Redundancy: 6.8 % / CC1/2: 0.992 / Net I/σ(I): 8.3
Reflection shellResolution: 3→3.107 Å / Num. unique obs: 859 / CC1/2: 0.717

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B5L

6b5l


Resolution: 3→36.79 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3167 472 5.13 %
Rwork0.2531 8729 -
obs0.256 9201 96.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.94 Å2 / Biso mean: 58.6783 Å2 / Biso min: 45.77 Å2
Refinement stepCycle: final / Resolution: 3→36.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3447 0 14 2 3463
Biso mean--59.91 55.22 -
Num. residues----451
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3-3.430.33471630.2993282795
3.43-4.320.35841460.261293198
4.32-5.40.28451630.2309297198

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