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- PDB-6lfv: Crystal structure of PCB4scFv(hN56D) -

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Basic information

Entry
Database: PDB / ID: 6lfv
TitleCrystal structure of PCB4scFv(hN56D)
ComponentsPCB4scFv(hN56D)
KeywordsIMMUNE SYSTEM / Co-PCB / antibody fragment
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNakamura, T. / Yamagata, Y. / Morioka, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: To Be Published
Title: Crystal structure of PCB4scFv(hN56D)
Authors: Nakamura, T. / Morioka, H.
History
DepositionDec 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 30, 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
A: PCB4scFv(hN56D)


Theoretical massNumber of molelcules
Total (without water)27,2371
Polymers27,2371
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10870 Å2
Unit cell
Length a, b, c (Å)92.420, 92.420, 53.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Antibody PCB4scFv(hN56D)


Mass: 27237.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.11 Å3/Da / Density % sol: 41.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: HEPES, PEG 8000, ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→32.78 Å / Num. obs: 41553 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 29.21 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 25.8
Reflection shellResolution: 1.9→1.95 Å / Rmerge(I) obs: 0.527 / Num. unique obs: 1322

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ESU

3esu


Resolution: 1.9→32.78 Å / SU ML: 0.2093 / Cross valid method: FREE R-VALUE / σ(F): 1.22 / Phase error: 23.7117
RfactorNum. reflection% reflection
Rfree0.2308 1775 5.12 %
Rwork0.1885 --
obs0.1907 34655 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.15 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 0 107 1894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00191825
X-RAY DIFFRACTIONf_angle_d0.52082475
X-RAY DIFFRACTIONf_chiral_restr0.0422278
X-RAY DIFFRACTIONf_plane_restr0.0038310
X-RAY DIFFRACTIONf_dihedral_angle_d13.719658
LS refinement shellResolution: 1.9→1.95 Å
RfactorNum. reflection% reflection
Rfree0.2858 156 -
Rwork0.2762 2496 -
obs--98.08 %

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