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- PDB-4lkx: Humanized antibody 4B12 Fab complexed with a CemX segment -

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Basic information

Entry
Database: PDB / ID: 4lkx
TitleHumanized antibody 4B12 Fab complexed with a CemX segment
Components
  • CemX segment
  • Fab fragment heavy chain
  • Fab fragment light chain
KeywordsIMMUNE SYSTEM / Immunoglobulin / antibody / Fab-peptide complex
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / immune response / extracellular space / plasma membrane
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoblobulin light chain / IGH@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsChu, H.M. / Wright, J. / Chan, Y.H. / Lin, C.J. / Chang, T.W. / Lim, C.
CitationJournal: Nat Commun / Year: 2014
Title: Two potential therapeutic antibodies bind to a peptide segment of membrane-bound IgE in different conformations.
Authors: Chu, H.M. / Wright, J. / Chan, Y.H. / Lin, C.J. / Chang, T.W. / Lim, C.
History
DepositionJul 9, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Nov 8, 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 20, 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
A: Fab fragment heavy chain
B: Fab fragment light chain
R: CemX segment


Theoretical massNumber of molelcules
Total (without water)49,0953
Polymers49,0953
Non-polymers00
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-29 kcal/mol
Surface area19640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.045, 107.156, 110.215
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Fab fragment heavy chain


Mass: 23790.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6GMX6*PLUS
#2: Antibody Fab fragment light chain


Mass: 23888.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q0KKI6*PLUS
#3: Protein/peptide CemX segment


Mass: 1415.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M sodium acetate trihydrate, 25% PEG 4000, 0.2M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.92→28.36 Å / Num. all: 38689 / Num. obs: 38689 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 29.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JIX, 3AAZ

2jix

3aaz


Resolution: 1.92→28.36 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.696 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22852 1934 5 %RANDOM
Rwork0.17967 ---
obs0.18212 36692 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.443 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å20 Å20 Å2
2--3.65 Å20 Å2
3----2.24 Å2
Refinement stepCycle: LAST / Resolution: 1.92→28.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3368 0 0 261 3629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023440
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.964669
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4975434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28224.419129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.35815548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8931513
X-RAY DIFFRACTIONr_chiral_restr0.1260.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.0212550
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.922→1.972 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 119 -
Rwork0.244 2365 -
obs--94.81 %

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