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- PDB-3cle: HIV neutralizing monoclonal antibody YZ23 -

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Basic information

Entry
Database: PDB / ID: 3cle
TitleHIV neutralizing monoclonal antibody YZ23
Components
  • Fab heavy chain
  • Fab light chain
KeywordsIMMUNE SYSTEM / HIV-1 / monoclonal antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJin, L. / Paul, S. / Symersky, J.
CitationJournal: To be Published
Title: HIV neutralizing monoclonal antibody YZ23
Authors: Nishiama, Y. / Planque, S. / Mitsuda, Y. / Taguchi, H. / Jin, L. / Symersky, J. / Boivin, S. / Salas, M. / Hanson, C. / Paul, S.
History
DepositionMar 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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 1.4Nov 13, 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: Fab light chain
H: Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)47,1512
Polymers47,1512
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-24.6 kcal/mol
Surface area19720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.290, 62.919, 135.172
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 light chain


Mass: 23678.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: hybridoma
#2: Antibody Fab heavy chain


Mass: 23473.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: hybridoma
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 16% PEG6000, 0.1 M HEPES, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.24 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 2.5→38.5 Å / Num. all: 16453 / Num. obs: 15906 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 30 Å2 / Rsym value: 0.09 / Net I/σ(I): 11.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5 % / Mean I/σ(I) obs: 3 / Rsym value: 0.11 / % possible all: 99

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Processing

Software
NameClassification
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KN2

1kn2


Resolution: 2.5→10 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 760 -random
Rwork0.225 ---
obs0.225 15337 97.4 %-
all-15753 --
Displacement parametersBiso mean: 31 Å2
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3284 0 0 70 3354
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0054
X-RAY DIFFRACTIONc_angle_deg1.22

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