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- PDB-8fpa: Structure of a chimeric antibody (Fab) fragment bound to de-N-ace... -

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Basic information

Entry
Database: PDB / ID: 8fpa
TitleStructure of a chimeric antibody (Fab) fragment bound to de-N-acetyl polysialic acid (dPSA)
Components
  • Chimeric antibody Fab fragment, Fd chain
  • Humanized antibody Fab fragment, light chain
KeywordsIMMUNE SYSTEM / antibody / Fab / polysialic acid / complex
Function / homologyACETIC ACID / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsBeernink, P.T. / Agirre, J. / Beernink, B.P. / Moe, G.R.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Structure of de-N-acetyl polysialic acid bound to an antibody Fab fragment
Authors: Beernink, P.T. / Agirre, J. / Beernink, B.P. / Moe, G.R.
History
DepositionJan 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chimeric antibody Fab fragment, Fd chain
B: Humanized antibody Fab fragment, light chain
C: Chimeric antibody Fab fragment, Fd chain
D: Humanized antibody Fab fragment, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,06124
Polymers96,1564
Non-polymers3,90620
Water7,332407
1
A: Chimeric antibody Fab fragment, Fd chain
B: Humanized antibody Fab fragment, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,29815
Polymers48,0782
Non-polymers2,22013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-21 kcal/mol
Surface area18620 Å2
MethodPISA
2
C: Chimeric antibody Fab fragment, Fd chain
D: Humanized antibody Fab fragment, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7639
Polymers48,0782
Non-polymers1,6867
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-26 kcal/mol
Surface area18660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.585, 71.437, 91.495
Angle α, β, γ (deg.)90, 92.954, 90
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Antibody , 2 types, 4 molecules ACBD

#1: Antibody Chimeric antibody Fab fragment, Fd chain


Mass: 24079.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Humanized antibody Fab fragment, light chain


Mass: 23997.982 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)

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Sugars , 1 types, 2 molecules

#3: Polysaccharide 5-amino-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid-(2-8)-3,5-dideoxy-5- ...5-amino-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid-(2-8)-3,5-dideoxy-5-(propanoylamino)-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid-(2-8)-3,5-dideoxy-5-(propanoylamino)-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid-(2-9)-3,5-dideoxy-5-propanamido-D-glycero-D-galacto-non-2-ulosonic acid


Type: oligosaccharide / Mass: 1183.075 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/3,4,3/[AOd21122h_5*NCCC/3=O][Aad21122h-2a_2-6_5*NCCC/3=O][Aad21122h-2a_2-6_5*N]/1-2-2-3/a8-b2_b8-c2_c8-d2WURCSPDB2Glycan 1.1.0
[][<C12N1O8>]{[(1+2)][a-D-Neup5N]{[(5+1)][<C3O1>]{}[(8+2)][a-D-Neup5N]{[(5+1)][<C3O1>]{}[(8+2)][a-D-Neup5N]{}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 425 molecules

#4: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 24% polyethylene glycol 1,500; 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→74.49 Å / Num. obs: 84628 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 33.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Net I/σ(I): 9.1
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 39278 / CC1/2: 0.364 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Servalcat0.4.105refinement
XDSdata reduction
SCALEPACKdata scaling
PHASER1.19.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6pe7

6pe7


Resolution: 1.83→74.49 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2297 1458 -
Rwork0.1856 83171 -
obs-84628 99.84 %
Displacement parametersBiso mean: 39.29 Å2
Baniso -1Baniso -2Baniso -3
1-2.90316975 Å20 Å2-2.27503165 Å2
2---1.75152163 Å20 Å2
3----1.15164812 Å2
Refinement stepCycle: LAST / Resolution: 1.83→74.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6567 0 263 407 7237
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONs_bond_nonh_d0.012470040.0119
X-RAY DIFFRACTIONs_angle_nonh_deg2.062395321.8254
X-RAY DIFFRACTIONs_dihedral_angle_1_deg7.39348745
X-RAY DIFFRACTIONs_dihedral_angle_2_deg6.45421475
X-RAY DIFFRACTIONs_dihedral_angle_3_deg10.6468164010
X-RAY DIFFRACTIONs_dihedral_angle_6_deg15.318432210
X-RAY DIFFRACTIONs_chiral_restr0.089311110.1309
X-RAY DIFFRACTIONs_planes0.010394520.02
X-RAY DIFFRACTIONs_nbd0.213697280.2
X-RAY DIFFRACTIONs_nbtor0.2259119520.2
X-RAY DIFFRACTIONs_hbond_nbd0.14823560.2
X-RAY DIFFRACTIONs_symmetry_nbd0.19071580.2
X-RAY DIFFRACTIONs_symmetry_hbond_nbd0.1733130.2
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.9290.35672060.301312061X-RAY DIFFRACTION99.71
1.929-2.0460.27152100.245611408X-RAY DIFFRACTION99.82
2.046-2.1870.25721840.20510762X-RAY DIFFRACTION99.85
2.187-2.3620.23571710.18810036X-RAY DIFFRACTION99.87
2.362-2.5880.22871620.18239253X-RAY DIFFRACTION99.92
2.588-2.8930.22451420.17178361X-RAY DIFFRACTION99.94
2.893-3.340.21841360.17027396X-RAY DIFFRACTION99.92
3.34-4.0890.22881100.16666260X-RAY DIFFRACTION99.91
4.089-5.7770.1823840.16634895X-RAY DIFFRACTION99.76
5.777-74.490.2561530.21752739X-RAY DIFFRACTION99.61

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