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- PDB-6uga: ch28/11 Fab (monoclinic form) -

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Basic information

Entry
Database: PDB / ID: 6uga
Titlech28/11 Fab (monoclinic form)
Components
  • ch28/11 Fab heavy chain
  • ch28/11 Fab light chain
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / CHIMERIC ANTIBODY / ANTIGEN BINDING FRAGMENT
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / methanesulfonic acid
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSoliman, C. / Ramsland, P.A.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: The terminal sialic acid of stage-specific embryonic antigen-4 has a crucial role in binding to a cancer-targeting antibody.
Authors: Soliman, C. / Chua, J.X. / Vankemmelbeke, M. / McIntosh, R.S. / Guy, A.J. / Spendlove, I. / Durrant, L.G. / Ramsland, P.A.
History
DepositionSep 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 5, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 11, 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: ch28/11 Fab light chain
H: ch28/11 Fab heavy chain
A: ch28/11 Fab light chain
B: ch28/11 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4635
Polymers92,3674
Non-polymers961
Water2,144119
1
L: ch28/11 Fab light chain
H: ch28/11 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2803
Polymers46,1842
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-23 kcal/mol
Surface area19070 Å2
MethodPISA
2
A: ch28/11 Fab light chain
B: ch28/11 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)46,1842
Polymers46,1842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-22 kcal/mol
Surface area19130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.224, 69.619, 93.876
Angle α, β, γ (deg.)90.000, 98.290, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody ch28/11 Fab light chain


Mass: 23166.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody ch28/11 Fab heavy chain


Mass: 23016.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: Chemical ChemComp-03S / methanesulfonic acid / Methanesulfonic acid


Mass: 96.106 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4O3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.7 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 4000, iso-Propanol, sodium HEPES

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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: 2.5→50 Å / Num. obs: 33478 / % possible obs: 98.1 % / Redundancy: 3.4 % / Rrim(I) all: 0.07 / Net I/σ(I): 14.4
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 5126 / Rrim(I) all: 0.48

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UG7

6ug7


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.929 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.473 / ESU R Free: 0.279
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2387 2000 6 %RANDOM
Rwork0.1643 ---
obs0.1686 33121 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 142.24 Å2 / Biso mean: 58.7148 Å2 / Biso min: 29.24 Å2
Baniso -1Baniso -2Baniso -3
1-2.26 Å20 Å20.97 Å2
2---2.48 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6371 0 5 119 6495
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.026535
X-RAY DIFFRACTIONr_bond_other_d00.026007
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.958888
X-RAY DIFFRACTIONr_angle_other_deg3.843313926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3285839
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15724.599237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.007151041
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2571517
X-RAY DIFFRACTIONr_chiral_restr0.0910.21008
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217342
X-RAY DIFFRACTIONr_gen_planes_other0.010.021435
X-RAY DIFFRACTIONr_mcbond_it4.5355.5683374
X-RAY DIFFRACTIONr_mcbond_other4.5345.5663373
X-RAY DIFFRACTIONr_mcangle_it6.7698.3374207
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 146 -
Rwork0.26 2283 -
all-2429 -
obs--98.86 %

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