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- PDB-4f57: Fab structure of a neutralizing antibody L1 from an early subtype... -

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Basic information

Entry
Database: PDB / ID: 4f57
TitleFab structure of a neutralizing antibody L1 from an early subtype A HIV-1 infected patient
Components
  • Heavy chain of Fab of a neutralizing antibody L1
  • Light chain of Fab of a neutralizing antibody L1
KeywordsIMMUNE SYSTEM / Ig / antibody / gp120
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPan, R.M. / Kong, X.P.
CitationJournal: Plos Pathog. / Year: 2013
Title: Viral Escape from Neutralizing Antibodies in Early Subtype A HIV-1 Infection Drives an Increase in Autologous Neutralization Breadth.
Authors: Murphy, M.K. / Yue, L. / Pan, R. / Boliar, S. / Sethi, A. / Tian, J. / Pfafferot, K. / Karita, E. / Allen, S.A. / Cormier, E. / Goepfert, P.A. / Borrow, P. / Robinson, J.E. / Gnanakaran, S. ...Authors: Murphy, M.K. / Yue, L. / Pan, R. / Boliar, S. / Sethi, A. / Tian, J. / Pfafferot, K. / Karita, E. / Allen, S.A. / Cormier, E. / Goepfert, P.A. / Borrow, P. / Robinson, J.E. / Gnanakaran, S. / Hunter, E. / Kong, X.P. / Derdeyn, C.A.
History
DepositionMay 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.2Nov 20, 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: Light chain of Fab of a neutralizing antibody L1
H: Heavy chain of Fab of a neutralizing antibody L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0243
Polymers46,9322
Non-polymers921
Water9,584532
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-24 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.101, 57.463, 60.038
Angle α, β, γ (deg.)90.00, 112.78, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-580-

HOH

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Components

#1: Antibody Light chain of Fab of a neutralizing antibody L1


Mass: 22482.826 Da / Num. of mol.: 1 / Fragment: light chain of L1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: Antibody Heavy chain of Fab of a neutralizing antibody L1


Mass: 24449.404 Da / Num. of mol.: 1 / Fragment: heavy chain of L1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 532 / 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: 2.58 Å3/Da / Density % sol: 52.27 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.17 M (NH4)2SO4, 0.085 M cacodylate pH 6.5, 25.5% (w/v) polyethylene glycol (PEG) 8000, and 15% (v/v) glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03319 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 27, 2011
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 1.7→41.5 Å / Num. all: 52788 / Num. obs: 50571 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.7→1.73 Å / % possible all: 81.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NH7

3nh7


Resolution: 1.7→41.5 Å / SU ML: 0.18 / σ(F): 1.36 / Phase error: 22.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2091 2567 5.08 %random
Rwork0.1865 ---
obs0.1877 50557 95.72 %-
all-52817 --
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.572 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.1969 Å20 Å2-4.3672 Å2
2---4.9677 Å2-0 Å2
3---3.7708 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3296 0 6 532 3834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073390
X-RAY DIFFRACTIONf_angle_d1.1144616
X-RAY DIFFRACTIONf_dihedral_angle_d12.4921194
X-RAY DIFFRACTIONf_chiral_restr0.073516
X-RAY DIFFRACTIONf_plane_restr0.005594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.73150.26591420.24292227X-RAY DIFFRACTION82
1.7315-1.76680.27561310.25372427X-RAY DIFFRACTION87
1.7668-1.80520.27481280.23922564X-RAY DIFFRACTION92
1.8052-1.84720.27431470.24092645X-RAY DIFFRACTION96
1.8472-1.89340.26541300.22022648X-RAY DIFFRACTION96
1.8934-1.94460.28171410.22422680X-RAY DIFFRACTION97
1.9446-2.00180.26491370.21892676X-RAY DIFFRACTION97
2.0018-2.06640.23431650.20782667X-RAY DIFFRACTION97
2.0664-2.14030.23691480.19882729X-RAY DIFFRACTION97
2.1403-2.2260.21381520.20722658X-RAY DIFFRACTION97
2.226-2.32730.29161490.20192706X-RAY DIFFRACTION98
2.3273-2.44990.2461260.20882745X-RAY DIFFRACTION98
2.4499-2.60340.25441540.19652731X-RAY DIFFRACTION98
2.6034-2.80440.18861420.19272747X-RAY DIFFRACTION98
2.8044-3.08650.18421520.17782726X-RAY DIFFRACTION98
3.0865-3.5330.17651460.16492783X-RAY DIFFRACTION99
3.533-4.45030.15221480.14842775X-RAY DIFFRACTION99
4.4503-41.52470.1811290.1682856X-RAY DIFFRACTION98

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