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

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Basic information

Entry
Database: PDB / ID: 3idi
TitleCrystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 Fab' fragment in complex with gp41 Peptide ALDKWNQ
Components
  • 2F5 Fab heavy chain
  • 2F5 Fab light chain
  • gp41 MPER peptide
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: 2.1 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 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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
A: 2F5 Fab light chain
B: 2F5 Fab heavy chain
C: gp41 MPER peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7696
Polymers49,4853
Non-polymers2843
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.500, 76.500, 94.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide gp41 MPER peptide


Mass: 874.960 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Antibody , 2 types, 2 molecules AB

#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)

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Non-polymers , 3 types, 212 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium citrate, pH 5.6, 16% 2-propanol, 16% PEG 4000, 0.1% Tween-20, 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: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 16, 2008
RadiationMonochromator: Rigaku optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 27454 / Num. obs: 25395 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 12.3 Å2 / Rsym value: 0.083 / Net I/σ(I): 25.3
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.392 / % possible all: 84.8

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→28.15 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1041152.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1278 5 %RANDOM
Rwork0.212 ---
all0.212 27454 --
obs0.212 25395 92.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.488 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 23 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å20 Å20 Å2
2---1.59 Å20 Å2
3----0.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.1→28.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3310 0 16 209 3535
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d28.5
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.132
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it2.82.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.266 211 5.6 %
Rwork0.238 3585 -
obs--84.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4gol.paramgol.top

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