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- PDB-9pz6: Anti-NANP Fab with G112T light chain mutation -

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Basic information

Entry
Database: PDB / ID: 9pz6
TitleAnti-NANP Fab with G112T light chain mutation
Components
  • IgG heavy chain
  • IgG light chain
KeywordsIMMUNE SYSTEM / NANP / antibody / Fab / lambda
Function / homologyDI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 8, 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

Downloads & links

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Assembly

Deposited unit
H: IgG heavy chain
L: IgG light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0106
Polymers47,5802
Non-polymers4294
Water8,863492
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-32 kcal/mol
Surface area19900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.974, 71.761, 137.364
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody IgG heavy chain


Mass: 24529.590 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 light chain


Mass: 23050.535 Da / Num. of mol.: 1 / Mutation: G111T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 4 types, 496 molecules

#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 200 mM ammonium acetate, 100 mM Bis-Tris-HCl, pH 5.5, 25% (w/v) PEG 3350

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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: Jun 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.7→39.3 Å / Num. obs: 51978 / % possible obs: 96.86 % / Redundancy: 13.1 % / Biso Wilson estimate: 17.4 Å2 / CC1/2: 0.994 / Net I/σ(I): 6.66
Reflection shellResolution: 1.7→1.761 Å / Num. unique obs: 3934 / CC1/2: 0.177

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.19.1_4122refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→39.3 Å / SU ML: 0.2605 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.7076
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2307 2542 5.05 %
Rwork0.1971 47830 -
obs0.1988 50372 96.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.47 Å2
Refinement stepCycle: LAST / Resolution: 1.7→39.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3324 0 28 492 3844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00743571
X-RAY DIFFRACTIONf_angle_d0.97514883
X-RAY DIFFRACTIONf_chiral_restr0.0649543
X-RAY DIFFRACTIONf_plane_restr0.008634
X-RAY DIFFRACTIONf_dihedral_angle_d17.06131277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.43691220.37792002X-RAY DIFFRACTION74.34
1.73-1.770.39551060.36062171X-RAY DIFFRACTION80.8
1.77-1.810.35431380.34572512X-RAY DIFFRACTION92.11
1.81-1.850.33511500.312616X-RAY DIFFRACTION97.53
1.85-1.890.33591460.28092686X-RAY DIFFRACTION99.26
1.89-1.950.32731350.2692722X-RAY DIFFRACTION99.65
1.95-20.27731420.25132689X-RAY DIFFRACTION99.86
2-2.070.30151310.24012715X-RAY DIFFRACTION100
2.07-2.140.25821670.22022720X-RAY DIFFRACTION99.93
2.14-2.230.25981400.21262712X-RAY DIFFRACTION100
2.23-2.330.27371430.20312730X-RAY DIFFRACTION99.93
2.33-2.450.23131490.20012746X-RAY DIFFRACTION99.97
2.45-2.610.22911380.19512732X-RAY DIFFRACTION99.97
2.61-2.810.27171400.19512746X-RAY DIFFRACTION99.93
2.81-3.090.19141480.18012761X-RAY DIFFRACTION99.93
3.09-3.540.17881460.16442795X-RAY DIFFRACTION99.93
3.54-4.450.16461540.1342802X-RAY DIFFRACTION99.9
4.45-39.30.16431470.1422973X-RAY DIFFRACTION99.87

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