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- PDB-7o2z: Crystal structure of the anti-PAS Fab 2.2 in complex with its epi... -

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Basic information

Entry
Database: PDB / ID: 7o2z
TitleCrystal structure of the anti-PAS Fab 2.2 in complex with its epitope peptide
Components
  • P/A#1 epitope peptide
  • anti-PAS Fab 2.2 chimeric heavy chain
  • anti-PAS Fab 2.2 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: 2.55 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

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Assembly

Deposited unit
L: anti-PAS Fab 2.2 chimeric light chain
H: anti-PAS Fab 2.2 chimeric heavy chain
P: P/A#1 epitope peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8334
Polymers49,7973
Non-polymers351
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-46 kcal/mol
Surface area19970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.996, 121.996, 138.437
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Antibody anti-PAS Fab 2.2 chimeric light chain


Mass: 24137.754 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 2.2 chimeric heavy chain


Mass: 24968.939 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 P/A#1 epitope peptide


Mass: 690.786 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: ACE in the peptide sequence is the residue code for N-terminal acetylation
Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 11% (w/v) PEG 6000 100 mM Tris/HCl pH 8 200 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 29, 2019 / Details: Si mirror
RadiationMonochromator: Si 111 Double-Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.55→34.63 Å / Num. obs: 17370 / % possible obs: 99.9 % / Redundancy: 26.176 % / Biso Wilson estimate: 28.843 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.209 / Rrim(I) all: 0.213 / Χ2: 0.91 / Net I/σ(I): 16.98 / Num. measured all: 454683 / Scaling rejects: 46
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
2.55-2.6525.1710.7365.1246969186618660.9490.751100
2.65-2.827.4990.5796.863276230123010.9780.59100
2.8-326.8440.4289.2364882241724170.9890.437100
3-3.526.0230.26114.9101776391239110.9960.266100
3.5-426.8760.1722.959584221722170.9980.174100
4-625.9440.12129.5383358321432130.9990.123100
6-824.9010.1424.76202208148120.9980.14399.8
8-1024.5530.08535.7473663003000.9990.087100
10-34.6321.7780.07738.0172523473330.9980.07996

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.14 Å34.61 Å
Translation4.14 Å34.61 Å

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Processing

Software
NameVersionClassification
XDS16.8.2013data reduction
XSCALEMar 15, 2019data scaling
PHASER2.8.3phasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QQ9

3qq9


Resolution: 2.55→34.63 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.903 / SU B: 8.659 / SU ML: 0.188 / SU R Cruickshank DPI: 0.6248 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.625 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2376 825 4.7 %RANDOM
Rwork0.1951 ---
obs0.1971 16545 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.92 Å2 / Biso mean: 27.208 Å2 / Biso min: 9.93 Å2
Baniso -1Baniso -2Baniso -3
1--2.27 Å20 Å2-0 Å2
2---2.27 Å20 Å2
3---4.53 Å2
Refinement stepCycle: final / Resolution: 2.55→34.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3418 0 1 124 3543
Biso mean--22.19 24.74 -
Num. residues----447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133521
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173120
X-RAY DIFFRACTIONr_angle_refined_deg1.3271.6434806
X-RAY DIFFRACTIONr_angle_other_deg1.1351.5697309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1295446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89624.241145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47915556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.771157
X-RAY DIFFRACTIONr_chiral_restr0.0450.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023933
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02692
LS refinement shellResolution: 2.55→2.616 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 66 -
Rwork0.262 1193 -
all-1259 -
obs--100 %

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