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- PDB-3idn: Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Anti... -

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Basic information

Entry
Database: PDB / ID: 3idn
TitleCrystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 Fab' fragment in complex with gp41 Peptide analog ELD(Paf)WAS
Components
  • 2F5 Fab heavy chain
  • 2F5 Fab light chain
  • gp41 MPER peptide analog
KeywordsIMMUNE SYSTEM / HIV-1 / gp41 / MPER / 2F5
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsJulien, J.-P. / Bryson, S. / Pai, E.F.
CitationJournal: J.Virol. / Year: 2009
Title: Crystallographic definition of the epitope promiscuity of the broadly neutralizing anti-human immunodeficiency virus type 1 antibody 2F5: vaccine design implications.
Authors: Bryson, S. / Julien, J.P. / Hynes, R.C. / Pai, E.F.
History
DepositionJul 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 26, 2025Group: 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2F5 Fab light chain
B: 2F5 Fab heavy chain
C: gp41 MPER peptide analog


Theoretical massNumber of molelcules
Total (without water)49,4913
Polymers49,4913
Non-polymers00
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.400, 65.000, 174.900
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 2F5 Fab light chain


Mass: 23363.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: Antibody 2F5 Fab heavy chain


Mass: 25245.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Protein/peptide gp41 MPER peptide analog


Mass: 881.929 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 3.35 Å3/Da / Density % sol: 63.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium acetate, pH 5.6, 1.4 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 16, 2005
RadiationMonochromator: Xenocs optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. all: 32222 / Num. obs: 30156 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 32 Å2 / Rsym value: 0.063
Reflection shellResolution: 2.25→2.39 Å / Rsym value: 0.236 / % possible all: 86.4

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Processing

Software
NameClassification
MAR345data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→19.79 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 970776.11 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1507 5 %RANDOM
Rwork0.22 ---
all0.22 32222 --
obs0.22 30156 93.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.8244 Å2 / ksol: 0.37434 e/Å3
Displacement parametersBiso mean: 34.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20 Å20 Å2
2--1.64 Å20 Å2
3----2.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.25→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3332 0 0 202 3534
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d28.5
X-RAY DIFFRACTIONc_improper_angle_d1
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.316 224 4.9 %
Rwork0.28 4331 -
obs--86.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.top
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4protein_paf.paramprotein_paf.top

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