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- PDB-9pz5: Native anti-NANP Fab -

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Basic information

Entry
Database: PDB / ID: 9pz5
TitleNative anti-NANP Fab
Components
  • IgG heavy chain
  • IgG lambda light chain
KeywordsIMMUNE SYSTEM / NANP / antibody / Fab / lambda
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 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

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Assembly

Deposited unit
H: IgG heavy chain
L: IgG lambda light chain


Theoretical massNumber of molelcules
Total (without water)47,5362
Polymers47,5362
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-33 kcal/mol
Surface area19710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.657, 72.785, 138.740
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

#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 lambda light chain


Mass: 23006.482 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM Tris-HCl, pH 7.0, 20% (w/v) PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 0.9686 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: May 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.39→29.67 Å / Num. obs: 35347 / % possible obs: 99.68 % / Redundancy: 13.3 % / Biso Wilson estimate: 42.56 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.34
Reflection shellResolution: 2.39→2.475 Å / Num. unique obs: 1840 / CC1/2: 0.948

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.19.1_4122refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→29.67 Å / SU ML: 0.3376 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.8453
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2564 3506 9.92 %
Rwork0.1939 31841 -
obs0.2 35347 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.16 Å2
Refinement stepCycle: LAST / Resolution: 2.39→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 0 100 3412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513456
X-RAY DIFFRACTIONf_angle_d0.84254725
X-RAY DIFFRACTIONf_chiral_restr0.0519529
X-RAY DIFFRACTIONf_plane_restr0.0064612
X-RAY DIFFRACTIONf_dihedral_angle_d16.84731225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.420.43611320.28911209X-RAY DIFFRACTION96.06
2.42-2.450.31751440.27831283X-RAY DIFFRACTION99.72
2.45-2.490.34811400.27921237X-RAY DIFFRACTION100
2.49-2.530.35721450.27161340X-RAY DIFFRACTION99.73
2.53-2.570.36621360.26861207X-RAY DIFFRACTION99.7
2.57-2.620.37251440.26281317X-RAY DIFFRACTION99.73
2.62-2.660.30891410.26111281X-RAY DIFFRACTION99.72
2.66-2.710.36881410.25181272X-RAY DIFFRACTION99.86
2.71-2.770.36281340.24831281X-RAY DIFFRACTION99.86
2.77-2.830.3441480.26171272X-RAY DIFFRACTION100
2.83-2.90.3511390.24231265X-RAY DIFFRACTION99.93
2.9-2.970.31431410.24121271X-RAY DIFFRACTION99.16
2.97-3.050.33481360.251296X-RAY DIFFRACTION99.86
3.05-3.140.27961390.22221244X-RAY DIFFRACTION99.78
3.14-3.240.26061380.2431306X-RAY DIFFRACTION99.86
3.24-3.350.29091370.22441248X-RAY DIFFRACTION99.71
3.35-3.490.30261430.20741306X-RAY DIFFRACTION99.52
3.49-3.650.26381390.19331267X-RAY DIFFRACTION99.93
3.65-3.840.21911400.18451278X-RAY DIFFRACTION99.93
3.84-4.080.19941410.16911286X-RAY DIFFRACTION100
4.08-4.390.18291370.13421262X-RAY DIFFRACTION99.86
4.39-4.830.18731410.13251280X-RAY DIFFRACTION99.65
4.83-5.530.2081430.13891282X-RAY DIFFRACTION100
5.53-6.950.22521450.16671273X-RAY DIFFRACTION100
6.95-29.670.17961420.15041278X-RAY DIFFRACTION99.79

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