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- PDB-1nld: FAB FRAGMENT OF A NEUTRALIZING ANTIBODY DIRECTED AGAINST AN EPITO... -

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Basic information

Entry
Database: PDB / ID: 1nld
TitleFAB FRAGMENT OF A NEUTRALIZING ANTIBODY DIRECTED AGAINST AN EPITOPE OF GP41 FROM HIV-1
Components(FAB1583) x 2
KeywordsIMMUNOGLOBULIN / FAB FRAGMENT
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsDavies, C. / Beauchamp, J.C. / Emery, D. / Rawas, A. / Muirhead, H.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Structure of the Fab fragment from a neutralizing monoclonal antibody directed against an epitope of gp41 from HIV-1.
Authors: Davies, C. / Beauchamp, J.C. / Emery, D. / Rawas, A. / Muirhead, H.
#1: Journal: Nature / Year: 1989
Title: An Engineered Poliovirus Chimaera Elicits Broadly Reactive HIV-1 Neutralizing Antibodies
Authors: Evans, D.J. / Mckeating, J. / Meredith, J.M. / Burke, K.L. / Katrak, K. / John, A. / Ferguson, M. / Minor, P.D. / Weiss, R.A. / Almond, J.W.
History
DepositionJul 2, 1996Processing site: BNL
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: FAB1583
H: FAB1583


Theoretical massNumber of molelcules
Total (without water)47,1472
Polymers47,1472
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-21 kcal/mol
Surface area18580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.150, 82.550, 131.000
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 FAB1583


Mass: 24186.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: 1583 HYBRIDOMA / References: PIR: PC4203
#2: Antibody FAB1583


Mass: 22959.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: 1583 HYBRIDOMA
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 46 %
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 291 K / Method: vapor diffusion, hanging drop / PH range low: 5.5 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-25 %(w/v)PEG40001reservoir
2200 mMMES1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 8958 / % possible obs: 91.6 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.1016
Reflection
*PLUS
Highest resolution: 2.88 Å / Lowest resolution: 5.24 Å / Num. measured all: 27644

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Processing

Software
NameClassification
XENGENdata collection
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
X-PLORphasing
RefinementResolution: 2.9→8 Å / σ(F): 0
RfactorNum. reflection
Rfree0.326 -
Rwork0.198 -
obs0.198 8042
Displacement parametersBiso mean: 16.6 Å2
Refinement stepCycle: LAST / Resolution: 2.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 0 0 3312
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.7

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