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- PDB-9q0p: Human anti-EBV gH/gL Fab (AMMO1) with G111T light chain mutation -

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Basic information

Entry
Database: PDB / ID: 9q0p
TitleHuman anti-EBV gH/gL Fab (AMMO1) with G111T light chain mutation
Components
  • IgG heavy chain
  • IgG lambda light chain
KeywordsIMMUNE SYSTEM / EBV / antibody / Fab / lambda
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsYoung, T.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Comput Struct Biotechnol J / Year: 2025
Title: Single-residue engineering of lambda ( lambda ) antibody light chains reduces conformational flexibility and enhances thermal stability.
Authors: Jewel, Y. / Young, T. / Park, M. / Ly, K. / Gonzalez, A. / Mallett, T.C. / Williams, J.C.
History
DepositionAug 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IgG heavy chain
B: IgG lambda light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3483
Polymers47,2562
Non-polymers921
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-23 kcal/mol
Surface area19570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.722, 69.774, 124.659
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody IgG heavy chain


Mass: 24115.986 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 IgG lambda light chain


Mass: 23139.566 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 170 mM ammonium acetate, 85 mM sodium citrate-HCl, pH 5.6, 25.5% (w/v) PEG 4000, and 15% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.08→39.34 Å / Num. obs: 26825 / % possible obs: 98.53 % / Redundancy: 2 % / CC1/2: 0.998 / Net I/σ(I): 15.22
Reflection shellResolution: 2.083→2.157 Å / Num. unique obs: 2491 / CC1/2: 0.874

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→39.34 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2427 2000 7.46 %
Rwork0.1894 --
obs0.1933 26824 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.08→39.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3280 0 6 358 3644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063420
X-RAY DIFFRACTIONf_angle_d0.854681
X-RAY DIFFRACTIONf_dihedral_angle_d15.6741222
X-RAY DIFFRACTIONf_chiral_restr0.054527
X-RAY DIFFRACTIONf_plane_restr0.006604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.130.30961280.25131590X-RAY DIFFRACTION90
2.14-2.190.29551430.23911778X-RAY DIFFRACTION100
2.19-2.260.30351410.2391748X-RAY DIFFRACTION100
2.26-2.330.29861440.21931780X-RAY DIFFRACTION100
2.33-2.410.27611410.22161759X-RAY DIFFRACTION100
2.41-2.510.2811430.21621775X-RAY DIFFRACTION100
2.51-2.620.25961430.2111771X-RAY DIFFRACTION100
2.62-2.760.29751420.21151764X-RAY DIFFRACTION99
2.76-2.940.27041440.20571791X-RAY DIFFRACTION100
2.94-3.160.25471460.20941796X-RAY DIFFRACTION99
3.16-3.480.24341390.19211740X-RAY DIFFRACTION97
3.48-3.980.21391450.16811800X-RAY DIFFRACTION99
3.98-5.020.18271460.13521805X-RAY DIFFRACTION98
5.02-39.340.19311550.16331927X-RAY DIFFRACTION99

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