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- PDB-1p4i: Crystal Structure of scFv against peptide GCN4 -

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Basic information

Entry
Database: PDB / ID: 1p4i
TitleCrystal Structure of scFv against peptide GCN4
Components
  • ANTIBODY VARIABLE LIGHT CHAIN
  • antibody variable heavy chain
KeywordsIMMUNE SYSTEM / peptide binder / scFv / picomolar binder
Function / homology
Function and homology information


immunoglobulin mediated immune response / immunoglobulin complex / antigen binding / adaptive immune response / immune response / extracellular region / plasma membrane
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 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 lambda-1 chain V region / Ig heavy chain V region PJ14
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZahnd, C. / Spinelli, S. / Luginbuhl, B. / Jermutus, L. / Amstutz, P. / Cambillau, C. / Pluckthun, A.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Directed in Vitro Evolution and Crystallographic Analysis of a Peptide-binding Single Chain Antibody Fragment (scFv) with Low Picomolar Affinity.
Authors: Zahnd, C. / Spinelli, S. / Amstutz, P. / Cambillau, C. / Pluckthun, A.
History
DepositionApr 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE an appropriate sequence database reference for chains L and H were not available at the ...SEQUENCE an appropriate sequence database reference for chains L and H were not available at the time of processing. The author states that the sequence has not been deposited in any sequence database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: ANTIBODY VARIABLE LIGHT CHAIN
H: antibody variable heavy chain


Theoretical massNumber of molelcules
Total (without water)26,7812
Polymers26,7812
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-11 kcal/mol
Surface area10240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.089, 60.533, 123.055
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 ANTIBODY VARIABLE LIGHT CHAIN / IG LAMBDA-1 CHAIN V REGION S43


Mass: 13333.484 Da / Num. of mol.: 1 / Mutation: N36S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: paK400 / Production host: Escherichia coli (E. coli) / References: UniProt: P01723
#2: Antibody antibody variable heavy chain


Mass: 13447.799 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: paK400 / Production host: Escherichia coli (E. coli) / References: UniProt: P01820
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: ammonium sulfate, sodium citrate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1999
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.8→24 Å / Num. obs: 6870 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 11.9
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.28 / % possible all: 96

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MFA

1mfa


Resolution: 2.8→12 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 706 -RANDOM
Rwork0.2 ---
obs0.2 6460 95.1 %-
all-6796 --
Refinement stepCycle: LAST / Resolution: 2.8→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1667 0 0 61 1728

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