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- PDB-1il1: Crystal structure of G3-519, an anti-HIV monoclonal antibody -

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Basic information

Entry
Database: PDB / ID: 1il1
TitleCrystal structure of G3-519, an anti-HIV monoclonal antibody
Components
  • monoclonal antibody G3-519 (heavy chain)
  • monoclonal antibody G3-519 (light chain)
KeywordsIMMUNE SYSTEM / Fab / beta sheet structure / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBerry, M.B. / Johnson, K.A. / Radding, W. / Fung, M. / Liou, R. / Phillips Jr., G.N.
CitationJournal: Proteins / Year: 2001
Title: Structure of an anti-HIV monoclonal Fab antibody fragment specific to a gp120 C-4 region peptide.
Authors: Berry, M.B. / Johnson, K.A. / Radding, W. / Fung, M. / Liou, R. / Phillips Jr., G.N.
History
DepositionMay 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
A: monoclonal antibody G3-519 (heavy chain)
B: monoclonal antibody G3-519 (light chain)


Theoretical massNumber of molelcules
Total (without water)48,0732
Polymers48,0732
Non-polymers00
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-25 kcal/mol
Surface area20200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.200, 84.300, 134.000
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 monoclonal antibody G3-519 (heavy chain)


Mass: 23559.076 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
Cell line: mouse myeloma line SP2/0 fused with antibody expressing B cells
#2: Antibody monoclonal antibody G3-519 (light chain)


Mass: 24514.133 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
Cell line: mouse myeloma line SP2/0 fused with antibody expressing B cells
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.18 Å3/Da / Density % sol: 43.69 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2M ammonium sulfate, 200mM sodium chloride, 100mM sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Details: used microseeding / PH range low: 6 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 Mammonium sulfate1reservoir
2200 mM1reservoirNaCl
3100 mMsodium citrate1reservoir

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 22, 1997
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→19.74 Å / Num. all: 18605 / Num. obs: 18605 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.505 / % possible all: 88.1
Reflection
*PLUS

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
CNS1refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.74 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 124012.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1833 9.9 %RANDOM
Rwork0.1883 ---
all0.187 29382 --
obs0.187 18605 83.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.51 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso mean: 35.8 Å2
Baniso -1Baniso -2Baniso -3
1--6.6 Å20 Å20 Å2
2--7 Å20 Å2
3----0.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3379 0 0 260 3639
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d27.3
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it3.12.5
X-RAY DIFFRACTIONc_mcangle_it4.53
X-RAY DIFFRACTIONc_scbond_it6.33
X-RAY DIFFRACTIONc_scangle_it83.5
LS refinement shellResolution: 2.19→2.33 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.351 250 9.9 %
Rwork0.288 2287 -
obs-2287 69 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.9 % / Rfactor Rfree: 0.247
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
X-RAY DIFFRACTIONc_mcbond_it3.12.5
X-RAY DIFFRACTIONc_scbond_it6.33
X-RAY DIFFRACTIONc_mcangle_it4.53
X-RAY DIFFRACTIONc_scangle_it83.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.351 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.288

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