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- PDB-2pw1: Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Anti... -

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Basic information

Entry
Database: PDB / ID: 2pw1
TitleCrystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 in complex with gp41 Peptide ELDKWNSL
Components
  • 2F5 Fab fragment heavy chain
  • 2F5 Fab fragment light chain
  • peptide epitope
KeywordsIMMUNE SYSTEM / HIV-1 / 2F5 / gp41 / neutralizing antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBryson, S. / Julien, J.-P. / Hynes, R.C. / 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
DepositionMay 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: 2F5 Fab fragment heavy chain
B: 2F5 Fab fragment light chain
C: peptide epitope


Theoretical massNumber of molelcules
Total (without water)49,3543
Polymers49,3543
Non-polymers00
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-26 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.100, 65.200, 175.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe heavy chain and the light chain of the antibody assemble to form the 2F5 Fab fragment. the biological unit is identical to the asymmetric unit.

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Components

#1: Antibody 2F5 Fab fragment heavy 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 fragment light chain


Mass: 24985.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Protein/peptide peptide epitope


Mass: 1005.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 3.36 Å3/Da / Density % sol: 63.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M NaCitrate, AS 1.6M, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→45 Å / Num. all: 21089 / Num. obs: 20317 / % possible obs: 96.3 % / Redundancy: 4.5 % / Biso Wilson estimate: 33.2 Å2 / Rsym value: 0.135
Reflection shellResolution: 2.6→2.76 Å / Mean I/σ(I) obs: 1.2 / Num. unique all: 2972 / Rsym value: 0.352

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Processing

Software
NameVersionClassification
CNS1refinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→43.78 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1201898.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1037 5.1 %RANDOM
Rwork0.213 ---
obs0.213 20317 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.9517 Å2 / ksol: 0.370182 e/Å3
Displacement parametersBiso mean: 25.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å20 Å2
2--3 Å20 Å2
3----2.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.6→43.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3381 0 0 174 3555
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d29
X-RAY DIFFRACTIONc_improper_angle_d1.41
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it2.12
X-RAY DIFFRACTIONc_scbond_it1.812
X-RAY DIFFRACTIONc_scangle_it2.712.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.362 163 5.2 %
Rwork0.3 2972 -
obs--90.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4

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