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- PDB-4gay: Structure of the broadly neutralizing antibody AP33 -

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Basic information

Entry
Database: PDB / ID: 4gay
TitleStructure of the broadly neutralizing antibody AP33
Components
  • NEUTRALIZING ANTIBODY AP33 HEAVY CHAIN
  • NEUTRALIZING ANTIBODY AP33 LIGHT CHAIN
KeywordsIMMUNE SYSTEM / antibody Fab / neutralizing antibody / HCV E2
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsPotter, J.A. / Owsianka, A. / Jeffery, N. / Matthews, D. / Keck, Z. / Lau, P. / Foung, S.K.H. / Taylor, G.L. / Patel, A.H.
CitationJournal: J.Virol. / Year: 2012
Title: Toward a Hepatitis C Virus Vaccine: the Structural Basis of Hepatitis C Virus Neutralization by AP33, a Broadly Neutralizing Antibody.
Authors: Potter, J.A. / Owsianka, A.M. / Jeffery, N. / Matthews, D.J. / Keck, Z.Y. / Lau, P. / Foung, S.K. / Taylor, G.L. / Patel, A.H.
History
DepositionJul 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: NEUTRALIZING ANTIBODY AP33 HEAVY CHAIN
L: NEUTRALIZING ANTIBODY AP33 LIGHT CHAIN
A: NEUTRALIZING ANTIBODY AP33 HEAVY CHAIN
B: NEUTRALIZING ANTIBODY AP33 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4986
Polymers95,1984
Non-polymers3002
Water1086
1
H: NEUTRALIZING ANTIBODY AP33 HEAVY CHAIN
L: NEUTRALIZING ANTIBODY AP33 LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)47,5992
Polymers47,5992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-24 kcal/mol
Surface area19460 Å2
MethodPISA
2
A: NEUTRALIZING ANTIBODY AP33 HEAVY CHAIN
B: NEUTRALIZING ANTIBODY AP33 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8994
Polymers47,5992
Non-polymers3002
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-27 kcal/mol
Surface area19330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.874, 90.874, 459.156
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
DetailsThe asymmetric unit contains two biological units

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Components

#1: Antibody NEUTRALIZING ANTIBODY AP33 HEAVY CHAIN


Mass: 23677.420 Da / Num. of mol.: 2 / Fragment: Fab fragment of AP33 heavy chain / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody NEUTRALIZING ANTIBODY AP33 LIGHT CHAIN


Mass: 23921.352 Da / Num. of mol.: 2 / Fragment: Fab fragment of AP33 light chain / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.49 Å3/Da / Density % sol: 50.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 18% PEG 8K, 0.1M TrisHCl, 0.2M CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 9, 2010
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. all: 29053 / Num. obs: 29053 / % possible obs: 95.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.65→2.8 Å / % possible all: 96.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→24.87 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.846 / SU B: 17.088 / SU ML: 0.359 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 4.287 / ESU R Free: 0.436 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32041 1436 5.2 %RANDOM
Rwork0.24339 ---
obs0.24731 26337 95.59 %-
all-29053 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.754 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å20 Å2
2--0.84 Å20 Å2
3----1.68 Å2
Refinement stepCycle: LAST / Resolution: 2.65→24.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6519 0 20 6 6545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226705
X-RAY DIFFRACTIONr_angle_refined_deg1.6031.9519158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7115840
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.88124.406261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.005151041
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8321524
X-RAY DIFFRACTIONr_chiral_restr0.1040.21052
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215020
X-RAY DIFFRACTIONr_mcbond_it0.671.54232
X-RAY DIFFRACTIONr_mcangle_it1.26826910
X-RAY DIFFRACTIONr_scbond_it1.58232473
X-RAY DIFFRACTIONr_scangle_it2.6934.52248
LS refinement shellResolution: 2.64→2.708 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.495 87 -
Rwork0.368 1681 -
obs--84.8 %

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