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- PDB-1jp5: Crystal structure of the single-chain Fv fragment 1696 in complex... -

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Basic information

Entry
Database: PDB / ID: 1jp5
TitleCrystal structure of the single-chain Fv fragment 1696 in complex with the epitope peptide corresponding to N-terminus of HIV-1 protease
Components
  • epitope peptide corresponding to N-terminus of HIV-1 protease
  • single-chain Fv fragment 1696
KeywordsIMMUNE SYSTEM / antibody-antigen complex / HIV PR inhibiting antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRezacova, P. / Lescar, J. / Brynda, J. / Fabry, M. / Horejsi, M. / Sedlacek, J. / Bentley, G.A.
CitationJournal: Structure / Year: 2001
Title: Structural basis of HIV-1 and HIV-2 protease inhibition by a monoclonal antibody.
Authors: Rezacova, P. / Lescar, J. / Brynda, J. / Fabry, M. / Horejsi, M. / Sedlacek, J. / Bentley, G.A.
History
DepositionAug 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 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
Revision 1.4Nov 13, 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
A: single-chain Fv fragment 1696
B: single-chain Fv fragment 1696
C: epitope peptide corresponding to N-terminus of HIV-1 protease
D: epitope peptide corresponding to N-terminus of HIV-1 protease


Theoretical massNumber of molelcules
Total (without water)56,1524
Polymers56,1524
Non-polymers00
Water95553
1
A: single-chain Fv fragment 1696
C: epitope peptide corresponding to N-terminus of HIV-1 protease


Theoretical massNumber of molelcules
Total (without water)28,0762
Polymers28,0762
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-6 kcal/mol
Surface area10560 Å2
MethodPISA
2
B: single-chain Fv fragment 1696
D: epitope peptide corresponding to N-terminus of HIV-1 protease


Theoretical massNumber of molelcules
Total (without water)28,0762
Polymers28,0762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-5 kcal/mol
Surface area10530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.490, 57.060, 91.040
Angle α, β, γ (deg.)90.00, 97.07, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Antibody single-chain Fv fragment 1696 / IgG1/kappa antibody / IMMUNOGLOBULIN


Mass: 26876.650 Da / Num. of mol.: 2 / Fragment: scFv1696
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
#2: Protein/peptide epitope peptide corresponding to N-terminus of HIV-1 protease


Mass: 1199.404 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: octamer PQITLWQR from the N-terminus of HIV-1 protease, R added to the C-terminus to increase solubility
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.09 Å3/Da / Density % sol: 41.07 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.05M tri-sodium citrate, 0.1M sodium phosphate, 24% PEG 3400, 0.2M ammonium sulphate, pH 5.5, VAPOR DIFFUSION, HANGING DROP at 292K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.05 Mtri-sodium citrate1reservoir
20.1 Msodium phosphate1reservoirpH5.5
324 %PEG34001reservoir
40.2 Mammonium sulfate1reservoir
514 mg/mlpeptide1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 12, 2000
RadiationMonochromator: sagitally focused Ge / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 12910 / Num. obs: 12620 / % possible obs: 96.7 % / Redundancy: 9.6 % / Biso Wilson estimate: 42.4 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 6.06
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.323 / % possible all: 92.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: variable domains of Fab 1696 (PDB code 1CL7)

1cl7


Resolution: 2.7→19.46 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 897041.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1286 10.3 %RANDOM
Rwork0.229 ---
all0.263 12910 --
obs0.229 12488 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 16.6893 Å2 / ksol: 0.317164 e/Å3
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1-3.12 Å20 Å27.18 Å2
2---5.29 Å20 Å2
3---2.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3764 0 0 53 3817
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d27
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it2.042
X-RAY DIFFRACTIONc_scbond_it1.612
X-RAY DIFFRACTIONc_scangle_it2.562.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.385 225 11.2 %
Rwork0.31 1785 -
obs-1168 93.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.3 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.385 / % reflection Rfree: 11.2 % / Rfactor Rwork: 0.31

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