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- PDB-6p79: Engineered single chain antibody C9+C14 ScFv -

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Basic information

Entry
Database: PDB / ID: 6p79
TitleEngineered single chain antibody C9+C14 ScFv
Components
  • Engineered antibody heavy chain
  • Engineered antibody light chain
KeywordsIMMUNE SYSTEM / Antibody Engineering
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.583 Å
AuthorsZhang, Y. / Li, W. / Marshall, N.
CitationJournal: Aiche J / Year: 2020
Title: Computer-based Engineering of Thermostabilized Antibody Fragments.
Authors: Lee, J. / Der, B.S. / Karamitros, C.S. / Li, W. / Marshall, N.M. / Lungu, O.I. / Miklos, A.E. / Xu, J. / Kang, T.H. / Lee, C.H. / Tan, B. / Hughes, R.A. / Jung, S.T. / Ippolito, G.C. / Gray, ...Authors: Lee, J. / Der, B.S. / Karamitros, C.S. / Li, W. / Marshall, N.M. / Lungu, O.I. / Miklos, A.E. / Xu, J. / Kang, T.H. / Lee, C.H. / Tan, B. / Hughes, R.A. / Jung, S.T. / Ippolito, G.C. / Gray, J.J. / Zhang, Y. / Kuhlman, B. / Georgiou, G. / Ellington, A.D.
History
DepositionJun 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Engineered antibody heavy chain
L: Engineered antibody light chain


Theoretical massNumber of molelcules
Total (without water)26,7992
Polymers26,7992
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-11 kcal/mol
Surface area10540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.282, 66.696, 74.955
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 Engineered antibody heavy chain


Mass: 12799.095 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody Engineered antibody light chain


Mass: 13999.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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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: 2.07 Å3/Da / Density % sol: 40.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris-HCl, pH 8.5, 15% PEG2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 29, 2014
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.58→40 Å / Num. obs: 31217 / % possible obs: 99.2 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 33.3
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 5.15 / Num. unique obs: 1287 / Rsym value: 0.327 / % possible all: 84.6

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3UMT

3umt


Resolution: 1.583→38.126 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.28
RfactorNum. reflection% reflection
Rfree0.2021 2000 6.47 %
Rwork0.1745 --
obs0.1763 30919 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.583→38.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1743 0 0 152 1895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061839
X-RAY DIFFRACTIONf_angle_d1.1392501
X-RAY DIFFRACTIONf_dihedral_angle_d13.428653
X-RAY DIFFRACTIONf_chiral_restr0.046268
X-RAY DIFFRACTIONf_plane_restr0.005325
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5831-1.62270.21091380.17432002X-RAY DIFFRACTION99
1.6227-1.66660.20941420.16842038X-RAY DIFFRACTION100
1.6666-1.71560.19621400.16152040X-RAY DIFFRACTION100
1.7156-1.7710.21361420.16032041X-RAY DIFFRACTION100
1.771-1.83430.19891400.16992027X-RAY DIFFRACTION100
1.8343-1.90770.21531420.16352050X-RAY DIFFRACTION100
1.9077-1.99460.19521410.16942039X-RAY DIFFRACTION100
1.9946-2.09970.20731410.16332053X-RAY DIFFRACTION100
2.0997-2.23130.20891450.17862075X-RAY DIFFRACTION100
2.2313-2.40350.18871400.18112038X-RAY DIFFRACTION100
2.4035-2.64530.2341440.1972092X-RAY DIFFRACTION100
2.6453-3.0280.20471440.19342077X-RAY DIFFRACTION100
3.028-3.81440.19861470.18032121X-RAY DIFFRACTION100
3.8144-38.13670.18471540.15962226X-RAY DIFFRACTION100

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