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- PDB-6p4c: HyHEL10 Fab carrying four heavy chain mutations (HyHEL10-4x): L4F... -

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Basic information

Entry
Database: PDB / ID: 6p4c
TitleHyHEL10 Fab carrying four heavy chain mutations (HyHEL10-4x): L4F, Y33H, S56N, and Y58F
Components
  • HyHEL10 Fab heavy chain
  • HyHEL10 Fab light chain
KeywordsIMMUNE SYSTEM / HyHEL10-4x / HyHEL10 / Fab / lysozyme-binder
Function / homology
Function and homology information


: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / 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 / Mainly Beta
Similarity search - Domain/homology
MAb 44B1 light chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 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 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: HyHEL10 Fab light chain
H: HyHEL10 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1499
Polymers47,9012
Non-polymers2487
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-81 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.556, 40.156, 93.649
Angle α, β, γ (deg.)90.000, 107.570, 90.000
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11L-406-

HOH

21H-439-

HOH

31H-459-

HOH

41H-464-

HOH

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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: 24347.918 Da / Num. of mol.: 1 / Mutation: L4F, Y33H, S56N, Y58F
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: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.57 Å3/Da / Density % sol: 52.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM citrate, pH 4.2, 1 M lithium chloride, 11% w/v 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: Mar 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.85→46.47 Å / Num. obs: 42030 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.022 / Rrim(I) all: 0.056 / Net I/σ(I): 16.8 / Num. measured all: 275598 / Scaling rejects: 7
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
1.85-1.8960.8621552325770.7780.3860.9472100
9.06-46.476.20.02724804030.9990.0120.02950.398.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.8 Å46.47 Å
Translation5.8 Å46.47 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3D9A

3d9a


Resolution: 1.85→46.47 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.39 / SU ML: 0.098 / SU R Cruickshank DPI: 0.1262 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.122
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2229 2089 5 %RANDOM
Rwork0.188 ---
obs0.1898 39937 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 101.25 Å2 / Biso mean: 38.431 Å2 / Biso min: 23.37 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å20 Å20.27 Å2
2--2.55 Å20 Å2
3----1.22 Å2
Refinement stepCycle: final / Resolution: 1.85→46.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3150 0 7 139 3296
Biso mean--56.42 42.99 -
Num. residues----420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133319
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172851
X-RAY DIFFRACTIONr_angle_refined_deg1.7831.6454561
X-RAY DIFFRACTIONr_angle_other_deg1.4241.5676637
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5935436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39322.687134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26715477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.3891512
X-RAY DIFFRACTIONr_chiral_restr0.0730.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023786
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02698
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 161 -
Rwork0.281 2906 -
all-3067 -
obs--99.93 %

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