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- PDB-9cr9: Crystal structure of MA6 Fab in complex with PfCSP repeat region ... -

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Basic information

Entry
Database: PDB / ID: 9cr9
TitleCrystal structure of MA6 Fab in complex with PfCSP repeat region peptide NPNA3
Components
  • Circumsporozoite protein (NPNA)3 repeat region peptide
  • MA6 Fab heavy chain
  • MA6 Fab light chain
KeywordsIMMUNE SYSTEM / circumsporozoite protein / PfCSP / CSP / protective / neutralizing / antibody / Fab
Function / homology: / side of membrane / plasma membrane / cytoplasm / Circumsporozoite protein
Function and homology information
Biological speciesHomo sapiens (human)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRush, S.A. / McLellan, J.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Repertoire, function, and structure of serological antibodies induced by the R21/Matrix-M malaria vaccine
Authors: McDaniel, J.R. / Voss, W.N. / Bowyer, G. / Rush, S.A. / Spencer, A.J. / Bellamy, D. / Goike, J. / Gregory, S. / King, C.R. / McLellan, J.S. / Hill, A.V.S. / Georgiou, G. / Ewer, K.J. / Ippolito, G.C.
History
DepositionJul 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MA6 Fab heavy chain
B: MA6 Fab light chain
C: Circumsporozoite protein (NPNA)3 repeat region peptide
H: MA6 Fab heavy chain
L: MA6 Fab light chain
P: Circumsporozoite protein (NPNA)3 repeat region peptide


Theoretical massNumber of molelcules
Total (without water)99,4686
Polymers99,4686
Non-polymers00
Water20,9331162
1
A: MA6 Fab heavy chain
B: MA6 Fab light chain
C: Circumsporozoite protein (NPNA)3 repeat region peptide


Theoretical massNumber of molelcules
Total (without water)49,7343
Polymers49,7343
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-31 kcal/mol
Surface area19250 Å2
MethodPISA
2
H: MA6 Fab heavy chain
L: MA6 Fab light chain
P: Circumsporozoite protein (NPNA)3 repeat region peptide


Theoretical massNumber of molelcules
Total (without water)49,7343
Polymers49,7343
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-31 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.600, 61.050, 152.999
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody MA6 Fab heavy chain


Mass: 25141.135 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody MA6 Fab light chain


Mass: 23385.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide Circumsporozoite protein (NPNA)3 repeat region peptide / CS


Mass: 1207.210 Da / Num. of mol.: 2 / Fragment: residues 134-145 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P05691
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1162 / 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: 2.19 Å3/Da / Density % sol: 43.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 27% PEG3350, 3% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→47.72 Å / Num. obs: 74608 / % possible obs: 93.33 % / Redundancy: 1.8 % / Biso Wilson estimate: 17.05 Å2 / CC1/2: 0.941 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.077 / Rrim(I) all: 0.1089 / Net I/σ(I): 5.93
Reflection shellResolution: 1.8→1.864 Å / Rmerge(I) obs: 0.4335 / Mean I/σ(I) obs: 2.14 / Num. unique obs: 7426 / CC1/2: 0.626 / Rpim(I) all: 0.4335 / Rrim(I) all: 0.613 / % possible all: 93.07

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→47.72 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2151 3706 4.97 %
Rwork0.1853 --
obs0.1868 74521 93.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6652 0 0 1162 7814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086812
X-RAY DIFFRACTIONf_angle_d0.9649273
X-RAY DIFFRACTIONf_dihedral_angle_d17.7842409
X-RAY DIFFRACTIONf_chiral_restr0.0641035
X-RAY DIFFRACTIONf_plane_restr0.0061186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.3181450.29452683X-RAY DIFFRACTION94
1.82-1.850.29391350.27112666X-RAY DIFFRACTION92
1.85-1.880.31411290.25672726X-RAY DIFFRACTION93
1.88-1.90.23981100.25052710X-RAY DIFFRACTION93
1.9-1.930.27491520.24422493X-RAY DIFFRACTION86
1.93-1.960.32081240.22782639X-RAY DIFFRACTION91
1.96-20.23391770.21332698X-RAY DIFFRACTION95
2-2.030.25771420.22012854X-RAY DIFFRACTION96
2.03-2.070.23791580.22672692X-RAY DIFFRACTION95
2.07-2.120.25121270.2112767X-RAY DIFFRACTION94
2.12-2.160.25731330.19612710X-RAY DIFFRACTION94
2.16-2.210.23611640.2012670X-RAY DIFFRACTION92
2.21-2.270.26311320.2062634X-RAY DIFFRACTION91
2.27-2.330.26311060.20842567X-RAY DIFFRACTION85
2.33-2.40.22211420.19732595X-RAY DIFFRACTION91
2.4-2.480.25321450.20182770X-RAY DIFFRACTION95
2.48-2.560.22491560.20272776X-RAY DIFFRACTION95
2.56-2.670.2361400.19432789X-RAY DIFFRACTION95
2.67-2.790.2571400.19282718X-RAY DIFFRACTION94
2.79-2.930.21481480.18232778X-RAY DIFFRACTION94
2.93-3.120.19551300.17512629X-RAY DIFFRACTION91
3.12-3.360.20171560.16782924X-RAY DIFFRACTION99
3.36-3.70.16171940.15462817X-RAY DIFFRACTION98
3.7-4.230.16911360.14472799X-RAY DIFFRACTION94
4.23-5.330.1671340.12742804X-RAY DIFFRACTION94
5.33-47.720.16541510.16662907X-RAY DIFFRACTION95

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