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

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Basic information

Entry
Database: PDB / ID: 1svz
TitleCrystal structure of the single-chain Fv fragment 1696 in complex with the epitope peptide corresponding to N-terminus of HIV-2 protease
Components
  • epitope peptide corresponding to N-terminus of HIV-2 protease
  • single-chain Fv fragment 1696
KeywordsIMMUNE SYSTEM / antibody-antigen complex / HIV inhibiting antibody
Function / homology
Function and homology information


immunoglobulin complex / antigen binding / adaptive immune response / immune response
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig kappa chain V-II region 26-10
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsRezacova, P. / Brynda, J. / Lescar, J. / Bentley, G.A. / Fabry, M. / Horejsi, M. / Sedlacek, J.
CitationJournal: J.Struct.Biol. / Year: 2005
Title: Crystal structure of a cross-reaction complex between an anti-HIV-1 protease antibody and an HIV-2 protease peptide
Authors: Rezacova, P. / Brynda, J. / Lescar, J. / Fabry, M. / Horejsi, M. / Sieglova, I. / Sedlacek, J. / Bentley, G.A.
History
DepositionMar 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 1.4Oct 30, 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
A: single-chain Fv fragment 1696
B: single-chain Fv fragment 1696
C: epitope peptide corresponding to N-terminus of HIV-2 protease
D: epitope peptide corresponding to N-terminus of HIV-2 protease


Theoretical massNumber of molelcules
Total (without water)55,8804
Polymers55,8804
Non-polymers00
Water6,395355
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.184, 56.413, 88.304
Angle α, β, γ (deg.)90.00, 102.13, 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)
Description: T7 promoter-driven plasmid, inclusion bodies production followed by protein in vitro refolding
Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P01631
#2: Protein/peptide epitope peptide corresponding to N-terminus of HIV-2 protease


Mass: 1063.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: octapeptide PQFSLWKR
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 1.85 Å3/Da / Density % sol: 33.1 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: protein concentration 14mg/ml, 0.05M tri-sodium citrate, 0.1M sodium phosphate, 27% PEG 3400, 0.2M ammonium sulfate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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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: Jun 14, 2001
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: 1.88→30 Å / Num. all: 35996 / Num. obs: 34737 / % possible obs: 96.5 % / Redundancy: 8.2 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 16.88
Reflection shellResolution: 1.88→1.99 Å / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 1.5 / % possible all: 77.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JP5

1jp5


Resolution: 1.89→19.79 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1358407.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1621 5 %RANDOM
Rwork0.196 ---
obs0.1961 32745 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 71.3367 Å2 / ksol: 0.351579 e/Å3
Displacement parametersBiso mean: 41.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20 Å26.35 Å2
2---0.97 Å20 Å2
3----0.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 1.89→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3793 0 0 355 4148
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.729
X-RAY DIFFRACTIONc_angle_deg3.2
X-RAY DIFFRACTIONc_dihedral_angle_d27.2
X-RAY DIFFRACTIONc_improper_angle_d4.07
X-RAY DIFFRACTIONc_mcbond_it2.81.5
X-RAY DIFFRACTIONc_mcangle_it3.842
X-RAY DIFFRACTIONc_scbond_it3.742
X-RAY DIFFRACTIONc_scangle_it5.462.5
LS refinement shellResolution: 1.89→2 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.342 229 5.2 %
Rwork0.315 4201 -
obs--77.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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