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- PDB-7o31: Crystal structure of the anti-PAS Fab 1.2 in complex with its epi... -

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Basic information

Entry
Database: PDB / ID: 7o31
TitleCrystal structure of the anti-PAS Fab 1.2 in complex with its epitope peptide and the anti-Kappa VHH domain
Components
  • (anti-PAS Fab 1.2 chimeric ...) x 2
  • PAS#1 epitope peptide
  • anti-Kappa VHH domain
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)
Lama glama (llama)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsSchilz, J. / Schiefner, A. / 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 13, 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

Downloads & links

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Assembly

Deposited unit
L: anti-PAS Fab 1.2 chimeric light chain
H: anti-PAS Fab 1.2 chimeric heavy chain
X: anti-Kappa VHH domain
P: PAS#1 epitope peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9478
Polymers63,6994
Non-polymers2484
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-28 kcal/mol
Surface area24660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.296, 44.373, 93.032
Angle α, β, γ (deg.)90.000, 109.140, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein/peptide , 1 types, 1 molecules P

#4: Protein/peptide PAS#1 epitope peptide


Mass: 862.925 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)

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Antibody , 3 types, 3 molecules LHX

#1: Antibody anti-PAS Fab 1.2 chimeric light chain


Mass: 23870.518 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 1.2 chimeric heavy chain


Mass: 24774.693 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: Antibody anti-Kappa VHH domain


Mass: 14190.591 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 376 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.17 Å3/Da / Density % sol: 43.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 22% (w/v) PEG 3350 300 mM K-acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Nov 27, 2019
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.55→33.39 Å / Num. obs: 77314 / % possible obs: 97.2 % / Redundancy: 6.923 % / Biso Wilson estimate: 30.697 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.063 / Χ2: 0.872 / Net I/σ(I): 15.03 / Num. measured all: 535265 / Scaling rejects: 68
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
1.55-1.656.7770.9881.648784913533129630.7921.0795.8
1.65-1.87.0640.5263.1210223815026144740.9330.56796.3
1.8-27.2440.2217.469614613694132720.9870.23896.9
2-2.56.7370.09416.2711865918038176140.9960.10297.6
2.5-37.180.05229.4256773803979070.9990.05798.4
3-46.6860.03540.5542329641863310.9990.03898.6
4-66.4020.03145.5721210334233130.9990.03499.1
6-87.2310.03547.9659808388270.9990.03798.7
8-107.1110.03450.8821052982960.9980.03699.3
10-33.396.2330.03446.8119763473170.9990.03791.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.7 Å33.37 Å
Translation1.7 Å33.37 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDS16.8.2013data reduction
XSCALEMar 15, 2019data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7O2Z, 6ANA

7o2z

6ana


Resolution: 1.55→33.39 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.347 / SU ML: 0.08 / SU R Cruickshank DPI: 0.0922 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2323 3884 5 %RANDOM
Rwork0.1943 ---
obs0.1962 73508 97.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.16 Å2 / Biso mean: 26.694 Å2 / Biso min: 13.63 Å2
Baniso -1Baniso -2Baniso -3
1--1.53 Å20 Å2-0.99 Å2
2--0.44 Å20 Å2
3---1.43 Å2
Refinement stepCycle: final / Resolution: 1.55→33.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4343 0 16 372 4731
Biso mean--27.91 34.8 -
Num. residues----573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134566
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174030
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.6456217
X-RAY DIFFRACTIONr_angle_other_deg1.4031.5719417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.575594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.36122.5204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11315716
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9441521
X-RAY DIFFRACTIONr_chiral_restr0.0760.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025225
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02955
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 264 -
Rwork0.341 5344 -
all-5608 -
obs--95.85 %

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