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- PDB-1n4x: Structure of scFv 1696 at acidic pH -

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Basic information

Entry
Database: PDB / ID: 1n4x
TitleStructure of scFv 1696 at acidic pH
Components
  • immunoglobulin heavy chain variable region
  • immunoglobulin kappa chain variable region
KeywordsIMMUNE SYSTEM / immunoglobulin
Function / homology
Function and homology information


immunoglobulin complex / antigen binding / adaptive immune response / immune response / extracellular region
Similarity search - Function
: / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. ...: / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 / Anti-CEA 79 single chain Fv / :
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLescar, J. / Brynda, J. / Fabry, M. / Horejsi, M. / Rezacova, P. / Sedlacek, J. / Bentley, G.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of a single-chain Fv fragment of an antibody that inhibits the HIV-1 and HIV-2 proteases.
Authors: Lescar, J. / Brynda, J. / Fabry, M. / Horejsi, M. / Rezacova, P. / Sedlacek, J. / Bentley, G.A.
History
DepositionNov 2, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_validate_close_contact / software
Item: _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 ..._pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2
Revision 1.4Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 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

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Assembly

Deposited unit
L: immunoglobulin kappa chain variable region
H: immunoglobulin heavy chain variable region
M: immunoglobulin kappa chain variable region
I: immunoglobulin heavy chain variable region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0836
Polymers52,0124
Non-polymers712
Water9,548530
1
L: immunoglobulin kappa chain variable region
H: immunoglobulin heavy chain variable region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0413
Polymers26,0062
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-24 kcal/mol
Surface area10650 Å2
MethodPISA
2
M: immunoglobulin kappa chain variable region
I: immunoglobulin heavy chain variable region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0413
Polymers26,0062
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-25 kcal/mol
Surface area10470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.930, 61.210, 57.300
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 kappa chain variable region / scFv 1696 molecule 1 / monoclonal antibody 1696


Mass: 12452.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q99M37, UniProt: P01631*PLUS
#2: Antibody immunoglobulin heavy chain variable region / scFv 1696 molecule 2 / monoclonal antibody 1696


Mass: 13552.892 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q921A6
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 3

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 34.69 %
Crystal grow
*PLUS
Temperature: 291 K / pH: 7.3 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 Msodium citrate1reservoirpH3.5
217.5 %PEG40001reservoir
30.175 Mammonium sulfate1reservoir
45 mg/mlprotein1drop
510 mMTris-HCl1droppH7.3

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.99 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jan 6, 1998 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 20 Å / Num. obs: 45422 / % possible obs: 91 % / Redundancy: 4.89 % / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
% possible obs: 84.2 % / Redundancy: 3.34 % / Num. unique obs: 5930 / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 6.6

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Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2280 -RANDOM
Rwork0.227 ---
all0.227 49892 --
obs0.227 45422 91 %-
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3656 0 2 530 4188
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_d1.34
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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