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- PDB-1i3g: CRYSTAL STRUCTURE OF AN AMPICILLIN SINGLE CHAIN FV, FORM 1, FREE -

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Basic information

Entry
Database: PDB / ID: 1i3g
TitleCRYSTAL STRUCTURE OF AN AMPICILLIN SINGLE CHAIN FV, FORM 1, FREE
Components(ANTIBODY FV FRAGMENT) x 2
KeywordsANTIBIOTIC / ANTIBODY FV FRAGMENT
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsJung, S. / Spinelli, S. / Schimmele, B. / Honegger, A. / Pugliese, L. / Cambillau, C. / Pluckthun, A.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Selection, characterization and x-ray structure of anti-ampicillin single-chain Fv fragments from phage-displayed murine antibody libraries.
Authors: Burmester, J. / Spinelli, S. / Pugliese, L. / Krebber, A. / Honegger, A. / Jung, S. / Schimmele, B. / Cambillau, C. / Pluckthun, A.
History
DepositionFeb 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 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
L: ANTIBODY FV FRAGMENT
H: ANTIBODY FV FRAGMENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8953
Polymers25,7772
Non-polymers1181
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-23 kcal/mol
Surface area10250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.2, 62.2, 136.8
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number92
Space group name H-MP41212

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Components

#1: Antibody ANTIBODY FV FRAGMENT


Mass: 12295.677 Da / Num. of mol.: 1 / Fragment: VL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: PROTEIN SELECTED BY PHAGE DISPLAY / Production host: Escherichia coli (E. coli)
#2: Antibody ANTIBODY FV FRAGMENT


Mass: 13480.933 Da / Num. of mol.: 1 / Fragment: VH DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: PROTEIN SELECTED BY PHAGE DISPLAY / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.57 Å3/Da / Density % sol: 52.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Ammonium Sulfate,potassium phosphate, MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
116 mg/mlprotein1drop
21.75 Mammonium sulfate1drop
350 mMphosphate1droppH6.5
45 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.44→20 Å / Num. all: 41050 / Num. obs: 9809 / % possible obs: 89.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.07 / Net I/σ(I): 11
Reflection
*PLUS
Num. measured all: 41050
Reflection shell
*PLUS
% possible obs: 71.7 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: anti-N9-neuraminidase antibody NC41/anti-lysozyme antibody D11.15

Resolution: 2.44→15 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.243 -RANDOM
Rwork0.175 --
obs-9323 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.44→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1693 0 0 77 1770
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.81
X-RAY DIFFRACTIONx_improper_angle_d1.21
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / σ(F): 0 / Rfactor obs: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.811
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.213

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