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- PDB-9dss: Crystal structure of Fab 7088 in complex with NPNA3 peptide from ... -

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Basic information

Entry
Database: PDB / ID: 9dss
TitleCrystal structure of Fab 7088 in complex with NPNA3 peptide from circumsporozoite protein
Components
  • Circumsporozoite protein
  • Heavy chain of Fab 7088
  • Light Chain of Fab 7088
KeywordsIMMUNE SYSTEM / Antibody
Function / homology
Function and homology information


host cell surface binding / symbiont entry into host / entry into host cell by a symbiont-containing vacuole / heparan sulfate proteoglycan binding / side of membrane / cell surface / plasma membrane / cytoplasm
Similarity search - Function
: / Plasmodium circumsporozoite protein / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat
Similarity search - Domain/homology
Circumsporozoite protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJain, M. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
Bill & Melinda Gates FoundationINV-056202 United States
CitationJournal: To Be Published
Title: Crystal structure of Fab 7088 in complex with NPNA3 peptide from circumsporozoite protein
Authors: Jain, M. / Wilson, I.A.
History
DepositionSep 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Heavy chain of Fab 7088
B: Light Chain of Fab 7088
A: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)49,0483
Polymers49,0483
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-31 kcal/mol
Surface area19050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.114, 72.114, 195.786
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 Heavy chain of Fab 7088


Mass: 24274.373 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Light Chain of Fab 7088


Mass: 23566.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein/peptide Circumsporozoite protein / CS / PfCSP


Mass: 1207.210 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: CSP, PF3D7_0304600 / Production host: synthetic construct (others) / References: UniProt: Q7K740
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.59 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium chloride and 20% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 35785 / % possible obs: 99.65 % / Redundancy: 11.5 % / Biso Wilson estimate: 48.73 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.034 / Net I/σ(I): 61
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 2.42 / Num. unique obs: 3460 / CC1/2: 0.794 / Rpim(I) all: 0.794

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→26.93 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2625 2000 5.59 %
Rwork0.2286 --
obs0.2305 35785 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→26.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3317 0 0 19 3336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.935
X-RAY DIFFRACTIONf_dihedral_angle_d16.9911200
X-RAY DIFFRACTIONf_chiral_restr0.058515
X-RAY DIFFRACTIONf_plane_restr0.008591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.36951380.30772320X-RAY DIFFRACTION99
2.05-2.10.36021380.31542350X-RAY DIFFRACTION100
2.11-2.170.32161410.29092376X-RAY DIFFRACTION100
2.17-2.240.35481400.27962363X-RAY DIFFRACTION100
2.24-2.320.33231410.27692384X-RAY DIFFRACTION100
2.32-2.410.29651420.28532393X-RAY DIFFRACTION100
2.41-2.520.33411400.28142378X-RAY DIFFRACTION100
2.52-2.650.33891420.28942395X-RAY DIFFRACTION100
2.65-2.820.33461430.2772408X-RAY DIFFRACTION100
2.82-3.030.32721430.28562421X-RAY DIFFRACTION100
3.04-3.340.25761430.25882421X-RAY DIFFRACTION100
3.34-3.820.25171460.2292452X-RAY DIFFRACTION100
3.82-4.810.21511470.182480X-RAY DIFFRACTION99
4.81-26.930.21471560.18522644X-RAY DIFFRACTION100

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