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- PDB-7o33: Crystal structure of the anti-PAS Fab 3.1 in complex with its epi... -

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Basic information

Entry
Database: PDB / ID: 7o33
TitleCrystal structure of the anti-PAS Fab 3.1 in complex with its epitope peptide
Components
  • APSA epitope peptide
  • anti-PAS Fab 3.1 chimeric heavy chain
  • anti-PAS Fab 3.1 chimeric light chain
KeywordsIMMUNE SYSTEM / antibody / disordered protein antigen / PAS polypeptide / protein engineering
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsSchilz, J. / Skerra, A.
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Molecular recognition of structurally disordered Pro/Ala-rich sequences (PAS) by antibodies involves an Ala residue at the hot spot of the epitope.
Authors: Schilz, J. / Binder, U. / Friedrich, L. / Gebauer, M. / Lutz, C. / Schlapschy, M. / Schiefner, A. / Skerra, A.
History
DepositionApr 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 31, 2024Group: 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: anti-PAS Fab 3.1 chimeric light chain
H: anti-PAS Fab 3.1 chimeric heavy chain
P: APSA epitope peptide


Theoretical massNumber of molelcules
Total (without water)48,7413
Polymers48,7413
Non-polymers00
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-35 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.890, 61.280, 78.610
Angle α, β, γ (deg.)90.000, 106.350, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody anti-PAS Fab 3.1 chimeric light chain


Mass: 23972.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody anti-PAS Fab 3.1 chimeric heavy chain


Mass: 23660.537 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide APSA epitope peptide


Mass: 1108.159 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: PCA in the peptide sequence is the residue code for pyroglutamic acid
Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
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: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3350 200mM LiNO3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 26, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.85→45.61 Å / Num. obs: 36237 / % possible obs: 97.6 % / Redundancy: 3.019 % / Biso Wilson estimate: 36.495 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.083 / Χ2: 0.932 / Net I/σ(I): 9.21 / Num. measured all: 109397
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.953.1090.6242.1316637539353510.8020.74699.2
1.95-2.053.0650.3973.2313291436343360.9020.47699.4
2.05-2.152.9990.2754.5510674361335590.9410.33298.5
2.15-2.252.880.1995.738337303228950.9690.24395.5
2.25-2.53.0410.1437.6516395555453920.9820.17297.1
2.5-33.1110.08711.9619464632662560.990.10598.9
3-3.52.8880.05916.229056323631360.9930.07296.9
3.5-42.8010.05118.734815184017190.9930.06293.4
4-52.8090.04420.514759182216940.9950.05493
5-103.1710.038225235169116510.9970.04597.6
10-2030.02722.386632272210.9980.03297.4
20-302.8420.02621.2954211910.03190.5
30-45.612.1250.0318.77171180.9950.03872.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.42 Å45.61 Å
Translation4.42 Å45.61 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEJan 31, 2020data scaling
PHASER2.8.3phasing
REFMAC5.8.0266refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7O31

7o31


Resolution: 1.85→45.61 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.042 / SU ML: 0.142 / SU R Cruickshank DPI: 0.1673 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1812 5 %RANDOM
Rwork0.2094 ---
obs0.2113 34425 97.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.06 Å2 / Biso mean: 42.057 Å2 / Biso min: 21.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å22.01 Å2
2---2.45 Å2-0 Å2
3---1.46 Å2
Refinement stepCycle: final / Resolution: 1.85→45.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3367 0 0 197 3564
Biso mean---42.07 -
Num. residues----447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133462
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173171
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.6414723
X-RAY DIFFRACTIONr_angle_other_deg1.2691.5747371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0585448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81923.75136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87315553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.088159
X-RAY DIFFRACTIONr_chiral_restr0.0660.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023937
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02730
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 135 -
Rwork0.357 2564 -
all-2699 -
obs--99.34 %

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