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- PDB-3cmo: HIV neutralizing monoclonal antibody YZ18 -

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Basic information

Entry
Database: PDB / ID: 3cmo
TitleHIV neutralizing monoclonal antibody YZ18
Components
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
KeywordsIMMUNE SYSTEM / HIV-1 / monoclonal antibody
Function / homology
Function and homology information


Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin / 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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJin, L. / Prasad, V. / Paul, S.
CitationJournal: TO BE PUBLISHED
Title: HIV neutralizing monoclonal antibody YZ18
Authors: Jin, L. / Prasad, V. / Paul, S.
History
DepositionMar 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 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

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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
X: Fab light chain
Y: Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)94,4114
Polymers94,4114
Non-polymers00
Water1,54986
1
L: Fab light chain
H: Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)47,2052
Polymers47,2052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-25.8 kcal/mol
Surface area19280 Å2
MethodPISA
2
X: Fab light chain
Y: Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)47,2052
Polymers47,2052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-21.8 kcal/mol
Surface area19520 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8830 Å2
ΔGint-56.2 kcal/mol
Surface area37180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.650, 69.940, 84.360
Angle α, β, γ (deg.)90.00, 94.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab light chain / Fragment antigen-binding


Mass: 23264.598 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: hybridoma
#2: Antibody Fab heavy chain / Fragment antigen-binding


Mass: 23940.752 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: hybridoma / References: UniProt: Q6PJA7*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 47.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 18% PEG6000, 0.1 M sodium citrate, pH 5, 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: 2.3→50 Å / Num. all: 39214 / Num. obs: 37445 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 33 Å2 / Rsym value: 0.09 / Net I/σ(I): 5.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.95 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 4184 / Rsym value: 0.426 / % possible all: 95

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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 1YEH

1yeh


Resolution: 2.3→15 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.287 2025 -random
Rwork0.248 ---
all-39060 --
obs-37313 90.3 %-
Displacement parametersBiso mean: 39 Å2
Baniso -1Baniso -2Baniso -3
1-8.407 Å20 Å21.16 Å2
2---17.933 Å20 Å2
3---9.526 Å2
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6634 0 0 86 6720
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.0067
X-RAY DIFFRACTIONc_angle_deg1.238

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