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- PDB-1p4b: Three-Dimensional Structure Of a Single Chain Fv Fragment Complex... -

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Basic information

Entry
Database: PDB / ID: 1p4b
TitleThree-Dimensional Structure Of a Single Chain Fv Fragment Complexed With The peptide GCN4(7P-14P).
Components
  • Antibody Variable heavy chain
  • Antibody Variable light chain
  • GCN4(7P-14P) peptide
KeywordsIMMUNE SYSTEM / Fv antibody / antigen peptide binder / scFv / picomolar binder
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / adaptive immune response / immune response / extracellular space / 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 / Immunoglobulins / Immunoglobulin-like fold / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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.
History
DepositionApr 22, 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 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE an appropriate sequence database reference was not available for chains L, H, and P at the ...SEQUENCE an appropriate sequence database reference was not available for chains L, H, and P 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
P: GCN4(7P-14P) peptide


Theoretical massNumber of molelcules
Total (without water)28,1923
Polymers28,1923
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-23 kcal/mol
Surface area10310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.238, 36.291, 84.455
Angle α, β, γ (deg.)90.00, 90.50, 90.00
Int Tables number4
Space group name H-MP1211

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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
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: 13446.813 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: Protein/peptide GCN4(7P-14P) peptide


Mass: 1411.648 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED.
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.02 Å3/Da / Density % sol: 39.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, tris/HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293KK

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.988 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 10132 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 8.5
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1440 / Rsym value: 0.171 / % possible all: 97.2

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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: PDB ENTRY 1MFA

1mfa


Resolution: 2.35→15 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3 977 -RANDOM
Rwork0.219 ---
obs0.23 9599 98.3 %-
all-9629 --
Refinement stepCycle: LAST / Resolution: 2.35→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1765 0 0 111 1876

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