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- PDB-6p4a: HyHEL10 Fab complexed with hen egg lysozyme carrying two mutation... -

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Basic information

Entry
Database: PDB / ID: 6p4a
TitleHyHEL10 Fab complexed with hen egg lysozyme carrying two mutations (HEL2x-rigid): R21Q and R73E
Components
  • HyHEL10 Fab heavy chain
  • HyHEL10 Fab light chain
  • Lysozyme C
KeywordsHYDROLASE/IMMUNE SYSTEM / HyHEL10 / HEL2x-rigid / antibody-antigen / HyHEL10-HEL2x / HYDROLASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
: / Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Immunoglobulin V-Type ...: / Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Lysozyme / Lysozyme-like domain superfamily / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
MAb 44B1 light chain / Lysozyme C
Similarity search - Component
Biological speciesMus musculus (house mouse)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsLangley, D.B. / Christ, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Conformational diversity facilitates antibody mutation trajectories and discrimination between foreign and self-antigens.
Authors: Burnett, D.L. / Schofield, P. / Langley, D.B. / Jackson, J. / Bourne, K. / Wilson, E. / Porebski, B.T. / Buckle, A.M. / Brink, R. / Goodnow, C.C. / Christ, D.
History
DepositionMay 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: HyHEL10 Fab light chain
H: HyHEL10 Fab heavy chain
C: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)62,1553
Polymers62,1553
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-31 kcal/mol
Surface area23270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.622, 55.245, 74.234
Angle α, β, γ (deg.)90.000, 90.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody HyHEL10 Fab light chain


Mass: 23552.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: LC / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: A0A0E4B213
#2: Antibody HyHEL10 Fab heavy chain


Mass: 24327.902 Da / Num. of mol.: 1
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: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14274.016 Da / Num. of mol.: 1 / Mutation: R21Q, R73E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: P00698, lysozyme
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
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: 2.1 Å3/Da / Density % sol: 41.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM Bis-Tris propane, pH 7.0, 22% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→48.5 Å / Num. obs: 26223 / % possible obs: 99.4 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.039 / Rrim(I) all: 0.102 / Net I/σ(I): 11.9 / Num. measured all: 178665 / Scaling rejects: 17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.276.70.6491464821810.8990.2670.7032.797
9.07-48.56.50.03827144150.9990.0150.04137.699.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.49 Å48.5 Å
Translation2.49 Å48.5 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.2data scaling
PHASER2.8.2phasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3D9A

3d9a


Resolution: 2.2→48.5 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.174 / SU ML: 0.161 / SU R Cruickshank DPI: 0.0795 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.057
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2919 1204 4.6 %RANDOM
Rwork0.2289 ---
obs0.2317 25006 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 101.8 Å2 / Biso mean: 37.684 Å2 / Biso min: 20.11 Å2
Baniso -1Baniso -2Baniso -3
1--27.22 Å20 Å2-3.94 Å2
2--32.55 Å20 Å2
3----5.32 Å2
Refinement stepCycle: final / Resolution: 2.2→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4196 0 0 62 4258
Biso mean---33.98 -
Num. residues----552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134307
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173718
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.6425884
X-RAY DIFFRACTIONr_angle_other_deg1.2661.5718662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1645548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7222.798193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.20215652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6881519
X-RAY DIFFRACTIONr_chiral_restr0.0660.2586
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024860
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02901
LS refinement shellResolution: 2.201→2.258 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 77 -
Rwork0.419 1776 -
all-1853 -
obs--97.48 %

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