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- PDB-1mf2: ANTI HIV1 PROTEASE FAB COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1mf2
TitleANTI HIV1 PROTEASE FAB COMPLEX
Components(MONOCLONAL ANTIBODY F11.2.32) x 2
KeywordsIMMUNOGLOBULIN / FAB FRAGMENT / CROSS-REACTIVITY / HIV1 PROTEASE / ENZYME INHIBITION
Function / homology
Function and homology information


phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / immunoglobulin mediated immune response / complement activation, classical pathway / antigen binding ...phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / immunoglobulin mediated immune response / complement activation, classical pathway / antigen binding / positive regulation of phagocytosis / B cell differentiation / positive regulation of immune response / antibacterial humoral response / defense response to bacterium / external side of plasma membrane / extracellular space / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / : / Immunoglobulin kappa constant / Ig gamma-1 chain C region secreted form
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLescar, J. / Bentley, G.A.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Three-dimensional structure of an Fab-peptide complex: structural basis of HIV-1 protease inhibition by a monoclonal antibody.
Authors: Lescar, J. / Stouracova, R. / Riottot, M.M. / Chitarra, V. / Brynda, J. / Fabry, M. / Horejsi, M. / Sedlacek, J. / Bentley, G.A.
#1: Journal: Protein Sci. / Year: 1996
Title: Preliminary Crystallographic Studies of an Anti-HIV-1 Protease Antibody that Inhibits Enzyme Activity
Authors: Lescar, J. / Stouracova, R. / Riottot, M.M. / Chitarra, V. / Brynda, J. / Fabry, M. / Horejsi, M. / Sedlacek, J. / Bentley, G.A.
History
DepositionDec 27, 1996Processing site: BNL
Revision 1.0Dec 31, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
L: MONOCLONAL ANTIBODY F11.2.32
H: MONOCLONAL ANTIBODY F11.2.32
M: MONOCLONAL ANTIBODY F11.2.32
N: MONOCLONAL ANTIBODY F11.2.32


Theoretical massNumber of molelcules
Total (without water)95,9434
Polymers95,9434
Non-polymers00
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
M: MONOCLONAL ANTIBODY F11.2.32
N: MONOCLONAL ANTIBODY F11.2.32


Theoretical massNumber of molelcules
Total (without water)47,9712
Polymers47,9712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-25 kcal/mol
Surface area19340 Å2
MethodPISA
3
L: MONOCLONAL ANTIBODY F11.2.32
H: MONOCLONAL ANTIBODY F11.2.32


Theoretical massNumber of molelcules
Total (without water)47,9712
Polymers47,9712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-24 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.600, 94.700, 70.300
Angle α, β, γ (deg.)90.00, 105.80, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.32005, 0.01298, -0.94731), (0.01521, -0.99985, -0.00856), (-0.94728, -0.01167, -0.320206)24.18688, 23.8191, 33.95795
2given(0.32005, 0.01298, -0.94731), (0.01521, -0.99985, -0.00856), (-0.94728, -0.01167, -0.3202)24.18688, 23.8191, 33.95795

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Components

#1: Antibody MONOCLONAL ANTIBODY F11.2.32 / IMMUNOGLOBULIN / IGG1


Mass: 23635.109 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: HYBRIDOMA / Strain: BALB/C / References: GenBank: 600718, UniProt: P01837*PLUS
#2: Antibody MONOCLONAL ANTIBODY F11.2.32 / IMMUNOGLOBULIN / IGG1


Mass: 24336.324 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: HYBRIDOMA / Strain: BALB/C / References: GenBank: 600716, UniProt: P01868*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16.5 mg/mlFab1drop
210 %PEG40001drop
30.05 Msodium citrate1drop
420 %PEG40001reservoir
50.1 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 3, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 25505 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 10
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.3 / % possible all: 93.4
Reflection
*PLUS
Num. measured all: 105230 / Rmerge(I) obs: 0.106
Reflection shell
*PLUS
% possible obs: 93.4 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FBI

1fbi


Resolution: 2.6→8 Å / Rfactor Rfree error: 0.03 / Data cutoff high absF: 100000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.307 333 5 %RANDOM
Rwork0.206 ---
obs0.206 -96 %-
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.25 Å
Luzzati d res low-7 Å
Luzzati sigma a0.25 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6622 0 0 235 6857
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.73
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.14
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.58
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.381.5
X-RAY DIFFRACTIONx_mcangle_it22
X-RAY DIFFRACTIONx_scbond_it22
X-RAY DIFFRACTIONx_scangle_it2.52.5
LS refinement shellResolution: 2.6→2.7 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.315 50 5 %
Rwork0.25 3371 -
obs--97 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 24344 / Rfactor all: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.14
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.58
LS refinement shell
*PLUS
Rfactor obs: 0.25

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