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- PDB-5gs3: Crystal structure of diabody -

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Basic information

Entry
Database: PDB / ID: 5gs3
TitleCrystal structure of diabody
Componentsdiabody proteinSingle-chain variable fragment
KeywordsIMMUNE SYSTEM / diabody / antibody fragment
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.698 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
H: diabody protein
A: diabody protein


Theoretical massNumber of molelcules
Total (without water)53,3592
Polymers53,3592
Non-polymers00
Water7,512417
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-28 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.955, 78.454, 59.913
Angle α, β, γ (deg.)90.00, 89.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody diabody protein / Single-chain variable fragment


Mass: 26679.592 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.76 Å3/Da / Density % sol: 55.37 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium sulfate, 10% PEG 8000

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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: 1.7→50 Å / Num. obs: 56450 / % possible obs: 99.1 % / Redundancy: 6.4 % / Net I/σ(I): 38.7
Reflection shellResolution: 1.7→1.76 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: 1.698→27.986 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 22.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2112 1984 3.52 %
Rwork0.1919 --
obs0.1927 56429 95.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.698→27.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3394 0 0 417 3811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063474
X-RAY DIFFRACTIONf_angle_d0.8534714
X-RAY DIFFRACTIONf_dihedral_angle_d11.3472014
X-RAY DIFFRACTIONf_chiral_restr0.056514
X-RAY DIFFRACTIONf_plane_restr0.004596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6982-1.74070.2771170.283547X-RAY DIFFRACTION87
1.7407-1.78770.26181410.25813707X-RAY DIFFRACTION91
1.7877-1.84030.27881260.27283731X-RAY DIFFRACTION92
1.8403-1.89970.23781430.24133757X-RAY DIFFRACTION93
1.8997-1.96760.2221360.22983784X-RAY DIFFRACTION94
1.9676-2.04640.18081380.19923895X-RAY DIFFRACTION95
2.0464-2.13950.24321460.18643927X-RAY DIFFRACTION96
2.1395-2.25220.25361530.19173957X-RAY DIFFRACTION97
2.2522-2.39330.25331340.19763981X-RAY DIFFRACTION98
2.3933-2.57790.23911430.19323993X-RAY DIFFRACTION98
2.5779-2.83710.18661600.19224017X-RAY DIFFRACTION99
2.8371-3.24710.24561420.19734057X-RAY DIFFRACTION99
3.2471-4.0890.16451460.17394078X-RAY DIFFRACTION99
4.089-27.98950.19291590.16724014X-RAY DIFFRACTION97

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