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- PDB-7rqp: Structure of PfCSP NPNV binding antibody L9 -

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Basic information

Entry
Database: PDB / ID: 7rqp
TitleStructure of PfCSP NPNV binding antibody L9
Components
  • L9 Heavy Chain
  • L9 Kappa Chain
KeywordsIMMUNE SYSTEM / Malaria / Antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsHurlburt, N.K. / Pancera, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation United States
CitationJournal: Cell Rep / Year: 2022
Title: The light chain of the L9 antibody is critical for binding circumsporozoite protein minor repeats and preventing malaria.
Authors: Wang, L.T. / Hurlburt, N.K. / Schon, A. / Flynn, B.J. / Flores-Garcia, Y. / Pereira, L.S. / Kiyuka, P.K. / Dillon, M. / Bonilla, B. / Zavala, F. / Idris, A.H. / Francica, J.R. / Pancera, M. / Seder, R.A.
History
DepositionAug 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 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: L9 Heavy Chain
B: L9 Kappa Chain


Theoretical massNumber of molelcules
Total (without water)48,0732
Polymers48,0732
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-24 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.964, 117.670, 143.665
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Antibody L9 Heavy Chain


Mass: 24475.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293E / Production host: Homo sapiens (human)
#2: Antibody L9 Kappa Chain


Mass: 23597.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293E / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.99 Å3/Da / Density % sol: 58.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Tris, pH 8.0, 100mM NaCl, 8% PEG 20,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.98→45.52 Å / Num. obs: 12137 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.027 / Rrim(I) all: 0.096 / Net I/σ(I): 17.5 / Num. measured all: 155768 / Scaling rejects: 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.98-3.1613.61.052611219190.8130.2951.0912.6100
8.94-45.5210.60.03653345020.9990.0120.03855.398.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D01

6d01


Resolution: 2.98→35.92 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.25 1204 9.98 %
Rwork0.1989 10861 -
obs0.2039 12065 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 301.17 Å2 / Biso mean: 113.2038 Å2 / Biso min: 42.24 Å2
Refinement stepCycle: final / Resolution: 2.98→35.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3229 0 0 3 3232
Biso mean---72.34 -
Num. residues----425
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.98-3.10.36091330.296511901323100
3.1-3.240.37721310.254211941325100
3.24-3.410.30961330.249712001333100
3.41-3.620.35361270.24561148127597
3.62-3.90.27871300.23091181131198
3.9-4.30.21681360.18512241360100
4.3-4.920.2031350.147512141349100
4.92-6.190.23391370.17712281365100
6.19-35.920.23321420.20041282142499
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)
10.5230.80420.04443.29880.89655.8889-0.29610.0696-0.0832-1.0557-0.0359-0.4822-0.39990.38590.23080.90410.00290.28470.82780.2080.8964-17.543.732-22.735
24.46890.5479-0.49026.68880.79365.0477-0.25810.1475-0.8634-0.1312-0.2064-0.50680.89030.40560.3810.65770.11780.18590.58310.14280.7321-20.402-14.263-9.072
32.19753.80260.55666.7447-0.29778.8240.06460.5491-0.1918-0.11260.07091.0842-1.7429-1.7357-0.30731.2050.42990.35111.2906-0.21751.2911-32.643-16.535-42.339
42.48390.5731-0.67311.69722.79636.99490.37350.28510.556-0.0786-0.32580.2061-0.1088-0.3419-0.07831.08680.20640.22640.7993-0.25061.1741-25.407-31.498-42.441
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:118 )A3 - 118
2X-RAY DIFFRACTION2( CHAIN B AND RESID 2:107 )B2 - 107
3X-RAY DIFFRACTION3( CHAIN A AND RESID 119:213 )A119 - 213
4X-RAY DIFFRACTION4( CHAIN B AND RESID 108:213 )B108 - 213

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