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- PDB-1e6o: Crystal structure of Fab13B5 against HIV-1 capsid protein p24 -

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Basic information

Entry
Database: PDB / ID: 1e6o
TitleCrystal structure of Fab13B5 against HIV-1 capsid protein p24
Components
  • IMMUNOGLOBULIN HEAVY CHAIN
  • IMMUNOGLOBULIN LIGHT CHAIN
KeywordsIMMUNOGLOBULIN / FAB / ANTIBODY / ANTIGEN / HIV-1 / P24 / CA
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMonaco-Malbet, S. / Berthet-Colominas, C. / Novelli, A. / Battai, N. / Piga, N. / Mallet, F. / Cusack, S.
CitationJournal: Structure / Year: 2000
Title: Mutual Conformational Adaptations in Antigen and Antibody Upon Complex Formation between an Fab and HIV-1 Capsid Protein P24
Authors: Monaco-Malbet, S. / Berthet-Colominas, C. / Novelli, A. / Battai, N. / Piga, N. / Cheynet, V. / Mallet, F. / Cusack, S.
History
DepositionAug 21, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Nov 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
H: IMMUNOGLOBULIN HEAVY CHAIN
L: IMMUNOGLOBULIN LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)46,8382
Polymers46,8382
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)36.680, 81.900, 134.400
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 IMMUNOGLOBULIN HEAVY CHAIN


Mass: 23552.301 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN 1-219 / Source method: isolated from a natural source / Details: OBTAINED BY PEPSIN CLEAVAGE (FAB') / Source: (natural) MUS MUSCULUS (house mouse)
#2: Antibody IMMUNOGLOBULIN LIGHT CHAIN


Mass: 23285.732 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN 1-210 / Source method: isolated from a natural source / Details: OBTAINED BY PEPSIN CLEAVAGE (FAB') / Source: (natural) MUS MUSCULUS (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 7MG/ML OF FAB'13B5 IN 0.1M PIPES PH=7.8 IN 9% TO 11% PEG8000 AFTER EQUILIBRATION IN HANGING DROPS AT 22C, pH 7.80
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19-11 %PEG80001reservoir
20.1 MPIPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.799
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.799 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. obs: 35964 / % possible obs: 94 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Biso Wilson estimate: 20.9 Å2 / Rsym value: 0.063
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3.5 % / Rsym value: 0.127 / % possible all: 85.4
Reflection
*PLUS
% possible obs: 94 % / Num. measured all: 124392 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 85.5 % / Rmerge(I) obs: 0.128

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Processing

Software
NameVersionClassification
X-PLOR3.8refinement
MOSFLMdata reduction
SCALAdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AFV

1afv


Resolution: 1.8→15 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
Details: LAST 4 AA OF L CHAIN ARE NOT SEQUENCED BUT PRESUMED TO BE RNEC
RfactorNum. reflection% reflectionSelection details
Rfree0.255 3569 9.9 %RANDOM
Rwork0.225 ---
obs0.225 35872 93.5 %-
Displacement parametersBiso mean: 27.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å20 Å20 Å2
2--3.45 Å20 Å2
3----5.44 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3276 0 0 237 3513
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.4
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_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.32 509 9.5 %
Rwork0.256 4839 -
obs--85 %
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
LS refinement shell
*PLUS
Rfactor Rfree: 0.32

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