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

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Basic information

Entry
Database: PDB / ID: 5grx
TitleCrystal structure of disulfide-bonded diabody
Componentsdiabody protein
KeywordsIMMUNE SYSTEM / diabody / antibody fragment / disulfide bonded
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 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 12, 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
Revision 1.2Oct 9, 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
G: diabody protein
H: diabody protein


Theoretical massNumber of molelcules
Total (without water)53,6572
Polymers53,6572
Non-polymers00
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-33 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.031, 99.608, 128.820
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 diabody protein


Mass: 26828.682 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


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 0.1 M Citric acid pH 3.5, 22% PEG 10000

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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: Sep 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 31720 / % possible obs: 96.3 % / Redundancy: 5.6 % / Net I/σ(I): 19
Reflection shellResolution: 2→2.07 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: 2.002→32.103 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 20.79
RfactorNum. reflection% reflection
Rfree0.2148 1583 5 %
Rwork0.1673 --
obs0.1697 31673 95.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.002→32.103 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3465 0 0 370 3835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063555
X-RAY DIFFRACTIONf_angle_d0.9044836
X-RAY DIFFRACTIONf_dihedral_angle_d11.1032055
X-RAY DIFFRACTIONf_chiral_restr0.06520
X-RAY DIFFRACTIONf_plane_restr0.005621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0024-2.0670.30131260.23562395X-RAY DIFFRACTION85
2.067-2.14090.24441390.21372638X-RAY DIFFRACTION94
2.1409-2.22660.26271390.19132639X-RAY DIFFRACTION94
2.2266-2.32790.24751410.18312675X-RAY DIFFRACTION95
2.3279-2.45060.21491420.18212713X-RAY DIFFRACTION97
2.4506-2.6040.26491430.18792709X-RAY DIFFRACTION97
2.604-2.8050.25331460.18192775X-RAY DIFFRACTION97
2.805-3.08710.22461480.17842798X-RAY DIFFRACTION98
3.0871-3.53330.21461480.15832830X-RAY DIFFRACTION99
3.5333-4.44970.18591530.13682895X-RAY DIFFRACTION100
4.4497-32.10750.16481580.153023X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 10.4894 Å / Origin y: 5.3021 Å / Origin z: 25.8396 Å
111213212223313233
T0.0953 Å2-0.0149 Å2-0.0015 Å2-0.0854 Å20.0208 Å2--0.1385 Å2
L0.953 °2-0.1635 °20.8172 °2-0.0617 °2-0.0703 °2--1.4973 °2
S-0.0498 Å °0.0057 Å °0.2143 Å °-0.007 Å °0.0057 Å °-0.0463 Å °-0.186 Å °0.0106 Å °0.0624 Å °
Refinement TLS groupSelection details: ALL

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