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- PDB-1nak: IGG1 FAB FRAGMENT (83.1) COMPLEX WITH 16-RESIDUE PEPTIDE (RESIDUE... -

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Basic information

Entry
Database: PDB / ID: 1nak
TitleIGG1 FAB FRAGMENT (83.1) COMPLEX WITH 16-RESIDUE PEPTIDE (RESIDUES 304-321 OF HIV-1 GP120 (MN ISOLATE))
Components
  • Fab 83.1 - heavy chain
  • Fab 83.1 - light chain
  • Peptide MP1
KeywordsIMMUNE SYSTEM / immunoglobulin fold
Function / homology
Function and homology information


Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane / identical protein binding
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsStanfield, R.L. / Ghiara, J.B. / Saphire, E.O. / Profy, A.T. / Wilson, I.A.
CitationJournal: Virology / Year: 2003
Title: Recurring conformation of the human immunodeficiency virus type 1 gp120 V3 loop.
Authors: Stanfield, R.L. / Ghiara, J.B. / Ollmann Saphire, E. / Profy, A.T. / Wilson, I.A.
History
DepositionNov 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 3, 2014Group: Structure summary
Revision 1.4Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE The sequence of this protein was not deposited into any sequence database

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Fab 83.1 - light chain
H: Fab 83.1 - heavy chain
P: Peptide MP1
M: Fab 83.1 - light chain
I: Fab 83.1 - heavy chain
Q: Peptide MP1


Theoretical massNumber of molelcules
Total (without water)98,1476
Polymers98,1476
Non-polymers00
Water1,928107
1
L: Fab 83.1 - light chain
H: Fab 83.1 - heavy chain
P: Peptide MP1


Theoretical massNumber of molelcules
Total (without water)49,0743
Polymers49,0743
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-28 kcal/mol
Surface area19500 Å2
MethodPISA
2
M: Fab 83.1 - light chain
I: Fab 83.1 - heavy chain
Q: Peptide MP1


Theoretical massNumber of molelcules
Total (without water)49,0743
Polymers49,0743
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-28 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.511, 122.597, 69.464
Angle α, β, γ (deg.)90.00, 108.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab 83.1 - light chain


Mass: 24156.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: ASW
#2: Antibody Fab 83.1 - heavy chain


Mass: 23089.838 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: ASW
#3: Protein/peptide Peptide MP1


Mass: 1827.182 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The peptide was synthesized chemically; its sequence occurs in the MN HIV-1 viral isolate.
References: UniProt: P05877*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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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: 2.54 Å3/Da / Density % sol: 51.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.6M Na/K phosphate, 5% isopropanol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115.0 mg/mlprotein1drop
21.6 Msodium potassium phosphate1reservoir
35 %isopropanol1reservoirpH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.033 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 16, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.57→48.2 Å / Num. all: 29751 / Num. obs: 29751 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 42.1 Å2 / Rsym value: 0.115 / Net I/σ(I): 9.4
Reflection shellResolution: 2.57→2.66 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.394 / % possible all: 80
Reflection
*PLUS
Num. measured all: 87725 / Rmerge(I) obs: 0.115
Reflection shell
*PLUS
% possible obs: 80 % / Rmerge(I) obs: 0.394

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ACY

1acy


Resolution: 2.57→48.08 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: RESIDUES 128-135 OF CHAINS H AND I HAVE VERY WEAK ELECTRON DENSITY AND WERE GIVEN OCCUPANCY VALUES OF 0.0
RfactorNum. reflection% reflectionSelection details
Rfree0.326 1469 4.9 %RANDOM
Rwork0.288 ---
all-29740 --
obs-29740 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.5752 Å2 / ksol: 0.376389 e/Å3
Displacement parametersBiso mean: 29.3 Å2
Baniso -1Baniso -2Baniso -3
1-6.69 Å20 Å22.24 Å2
2---4.33 Å20 Å2
3----2.36 Å2
Refine analyzeLuzzati coordinate error free: 0.54 Å / Luzzati sigma a free: 0.55 Å
Refinement stepCycle: LAST / Resolution: 2.57→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6770 0 0 107 6877
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_improper_angle_d0.98
LS refinement shellResolution: 2.57→2.66 Å / Rfactor Rfree error: 0.066 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.525 -5.3 %
Rwork0.464 1061 -
obs--74.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Lowest resolution: 48.2 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.98

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