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- PDB-3iy1: Variable domains of the WAM of Fab B fitted into the cryoEM recon... -

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Basic information

Entry
Database: PDB / ID: 3iy1
TitleVariable domains of the WAM of Fab B fitted into the cryoEM reconstruction of the virus-Fab B complex
DescriptorFab B
KeywordsIMMUNE SYSTEM / cryoEM / neutralizing antibody / parvovirus / canine / feline / fab footprint
Specimen sourceRattus norvegicus / mammal / ドブネズミ, どぶねずみ /
MethodElectron microscopy (18 Å resolution / Particle / Single particle)
AuthorsHafenstein, S. / Bowman, V.D. / Sun, T. / Nelson, C.D. / Palermo, L.M. / Battisti, A.J. / Parrish, C.R. / Rossmann, M.G.
CitationJ. Virol., 2009, 83, 5556-5566

J. Virol., 2009, 83, 5556-5566 StrPapers
Structural comparison of different antibodies interacting with parvovirus capsids.
Susan Hafenstein / Valorie D Bowman / Tao Sun / Christian D S Nelson / Laura M Palermo / Paul R Chipman / Anthony J Battisti / Colin R Parrish / Michael G Rossmann

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 9, 2009 / Release: May 12, 2009
RevisionDateData content typeGroupProviderType
1.0May 12, 2009Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance

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Assembly

Deposited unit
A: Fab B, light chain
B: Fab B, heavy chain


Theoretical massNumber of molelcules
Total (without water)23,4172
Polyers23,4172
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Polypeptide(L)Fab B, light chain


Mass: 11643.067 Da / Num. of mol.: 1 / Fragment: antibody B fragment
Source: (natural) Rattus norvegicus / mammal / ドブネズミ, どぶねずみ /
#2: Polypeptide(L)Fab B, heavy chain


Mass: 11773.996 Da / Num. of mol.: 1
Source: (natural) Rattus norvegicus / mammal / ドブネズミ, どぶねずみ /

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

Component
IDNameTypeParent IDSynonym
1Fab fragment from MAb B interacting with feline panleukopenia virus (FPV)COMPLEX0
2feline panleukopenia virusVIRUS1FPV
Details of virusEmpty: NO / Enveloped: NO / Virus host category: VERTEBRATES / Virus isolate: STRAIN / Virus type: VIRION
Natural hostOrganism: Felis catus
Virus shellTriangulation number (T number): 1
Buffer solutionDetails: 10mM Tris / pH: 7.5
SpecimenConc.: 1 mg/ml / Details: 10mM Tris / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temp: 120 K / Method: blot before plunging

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Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM300FEG/T / Date: Jun 30, 2004
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 45000 / Calibrated magnification: 47190 / Nominal defocus max: 3.7 nm / Nominal defocus min: 1.7 nm / Camera length: 0 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: side mounted nitrogen cooled / Temperature: 93 kelvins / Temperature (max): 83 kelvins / Temperature (min): 83 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 28.4 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansSampling size: 7 microns / Details: scanned at 7 microns and bin averaged to 14 / Number digital images: 56 / Od range: 0.9 / Scanner model: ZEISS SCAI
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1EM3DRRECONSTRUCTION
2EMPFTRECONSTRUCTION
CTF correctionDetails: robem
SymmetryPoint symmetry: I
3D reconstructionMethod: common lines / Resolution: 18 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 1126 / Symmetry type: POINT
Number of atoms included #LASTProtein: 1648 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1648

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