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- PDB-5grz: Crystal structure of disulfide-bonded diabody -

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Basic information

Entry
Database: PDB / ID: 5grz
TitleCrystal structure of disulfide-bonded diabody
ComponentsdiabodySingle-chain variable fragment
KeywordsIMMUNE SYSTEM / diabody / antibody fragment / disulfide bond
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKim, J.H. / Song, D.H. / Youn, S.J. / Kim, J.W. / Cho, G. / Lee, H. / Lee, J.O.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
Ministry of Science, ICT and Future PlanningNRF-2014R1A2A1A10050436 Korea, Republic Of
Ministry of Health & WelfareHI15C1886 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2016
Title: Crystal structure of mono- and bi-specific diabodies and reduction of their structural flexibility by introduction of disulfide bridges at the Fv interface.
Authors: Kim, J.H. / Song, D.H. / Youn, S.J. / Kim, J.W. / Cho, G. / Kim, S.C. / Lee, H. / Jin, M.S. / Lee, J.O.
History
DepositionAug 13, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: diabody
A: diabody


Theoretical massNumber of molelcules
Total (without water)53,6692
Polymers53,6692
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-38 kcal/mol
Surface area19590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.841, 54.093, 54.725
Angle α, β, γ (deg.)90.00, 103.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody diabody / Single-chain variable fragment


Mass: 26834.643 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris HCl pH 8.5, 0.15 M Magnesium chloride, 32% PEG 3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 13288 / % possible obs: 98.7 % / Redundancy: 3.3 % / Net I/σ(I): 14.8
Reflection shellResolution: 2.7→2.8 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GS1

5gs1


Resolution: 2.7→28.957 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 35.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3012 722 5.6 %
Rwork0.2463 --
obs0.2493 12900 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→28.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3424 0 0 13 3437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113512
X-RAY DIFFRACTIONf_angle_d1.1754780
X-RAY DIFFRACTIONf_dihedral_angle_d12.8062040
X-RAY DIFFRACTIONf_chiral_restr0.057518
X-RAY DIFFRACTIONf_plane_restr0.006612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7002-2.90850.44161420.3622393X-RAY DIFFRACTION99
2.9085-3.20080.35341230.31832474X-RAY DIFFRACTION99
3.2008-3.66320.33031630.28322406X-RAY DIFFRACTION99
3.6632-4.61220.26871470.21662416X-RAY DIFFRACTION98
4.6122-28.95850.26381470.20062489X-RAY DIFFRACTION98

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