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- PDB-6x5e: Crystal structure of a Lewis-binding Fab (ch88.2) -

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Basic information

Entry
Database: PDB / ID: 6x5e
TitleCrystal structure of a Lewis-binding Fab (ch88.2)
Components
  • ch88.2 Fab heavy chain
  • ch88.2 Fab light chain
KeywordsIMMUNE SYSTEM / immunoglobulin / chimeric antibody / antigen binding fragment / Lewis-binding antibody
Function / homologyNICKEL (II) ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsSoliman, C. / Ramsland, P.A.
CitationJournal: Biochem.J. / Year: 2020
Title: Molecular and structural basis for Lewis glycan recognition by a cancer-targeting antibody.
Authors: Soliman, C. / Guy, A.J. / Chua, J.X. / Vankemmelbeke, M. / McIntosh, R.S. / Eastwood, S. / Truong, V.K. / Elbourne, A. / Spendlove, I. / Durrant, L.G. / Ramsland, P.A.
History
DepositionMay 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: ch88.2 Fab light chain
H: ch88.2 Fab heavy chain
A: ch88.2 Fab light chain
B: ch88.2 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3277
Polymers96,1514
Non-polymers1763
Water64936
1
L: ch88.2 Fab light chain
H: ch88.2 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1934
Polymers48,0762
Non-polymers1172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-38 kcal/mol
Surface area19930 Å2
MethodPISA
2
A: ch88.2 Fab light chain
B: ch88.2 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1343
Polymers48,0762
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-27 kcal/mol
Surface area19950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.423, 68.480, 91.750
Angle α, β, γ (deg.)110.495, 99.289, 90.006
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

#1: Antibody ch88.2 Fab light chain


Mass: 23644.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody ch88.2 Fab heavy chain


Mass: 24431.475 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.3 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG MME 200, Tris, Nickel (II) chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 44428 / % possible obs: 92.6 % / Redundancy: 1.8 % / Biso Wilson estimate: 60.41 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.07 / Net I/σ(I): 7.9
Reflection shellResolution: 2.29→2.4 Å / Num. unique obs: 6787 / CC1/2: 0.719 / Rrim(I) all: 0.88

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X80

4x80


Resolution: 2.29→33.49 Å / SU ML: 0.4361 / Cross valid method: FREE R-VALUE / σ(F): 1.87 / Phase error: 37.6612
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2841 1943 5.41 %RANDOM
Rwork0.2299 33993 --
obs0.2329 35936 92.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.4 Å2
Refinement stepCycle: LAST / Resolution: 2.29→33.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6658 0 3 36 6697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076816
X-RAY DIFFRACTIONf_angle_d1.00369268
X-RAY DIFFRACTIONf_chiral_restr0.05061041
X-RAY DIFFRACTIONf_plane_restr0.00571181
X-RAY DIFFRACTIONf_dihedral_angle_d9.9055923
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.350.38511360.34882414X-RAY DIFFRACTION93.54
2.35-2.410.38761400.33222470X-RAY DIFFRACTION93.21
2.41-2.480.34371420.33042407X-RAY DIFFRACTION92.72
2.48-2.560.42921260.3292470X-RAY DIFFRACTION91.6
2.56-2.650.38841410.33482335X-RAY DIFFRACTION91.26
2.65-2.760.41151310.31372481X-RAY DIFFRACTION92.46
2.76-2.880.34171370.29342450X-RAY DIFFRACTION93.8
2.89-3.040.34371480.28252464X-RAY DIFFRACTION94.57
3.04-3.230.32241560.26882486X-RAY DIFFRACTION93.85
3.23-3.480.33211400.25462363X-RAY DIFFRACTION91.22
3.48-3.830.3221370.23112416X-RAY DIFFRACTION91.11
3.83-4.380.25231390.20292365X-RAY DIFFRACTION91.49
4.38-5.510.20431320.16592450X-RAY DIFFRACTION92.35
5.51-33.490.23431380.19972422X-RAY DIFFRACTION92.65

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