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

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Basic information

Entry
Database: PDB / ID: 3clf
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 / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsSymersky, J. / Boivin, S. / Paul, S.
CitationJournal: To be Published
Title: HIV neutralizing monoclonal antibody YZ23
Authors: Nishiyama, 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 / Item: _software.name
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Fab light chain
H: Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)47,1862
Polymers47,1862
Non-polymers00
Water4,828268
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-32.3 kcal/mol
Surface area19870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.185, 63.134, 135.408
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: 23508.303 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.: 268 / Source method: isolated from a natural source / Formula: H2O

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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: 47.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 8% PEG6000, 0.1 M Tris, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.24 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 30712 / Num. obs: 30712 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 30 Å2 / Rsym value: 0.06 / Net I/σ(I): 13
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.8 % / Num. unique all: 2959 / Rsym value: 0.386 / % possible all: 97.8

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Processing

Software
NameClassification
MAR345data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3CLE

3cle


Resolution: 2→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.265 1523 random
Rwork0.22 --
all-31024 -
obs-30670 -
Displacement parametersBiso mean: 29.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.011 Å20 Å20 Å2
2---1.618 Å20 Å2
3---1.541 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3315 0 0 268 3583
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.37

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