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- PDB-5grv: Crystal structure of homo-specific diabody -

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Basic information

Entry
Database: PDB / ID: 5grv
TitleCrystal structure of homo-specific diabody
Components
  • homo-specific diabody heavy chain
  • homo-specific diabody light chain
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: 2.3 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
L: homo-specific diabody heavy chain
K: homo-specific diabody light chain


Theoretical massNumber of molelcules
Total (without water)26,8852
Polymers26,8852
Non-polymers00
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-13 kcal/mol
Surface area10410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.124, 134.124, 76.269
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11K-386-

HOH

21K-397-

HOH

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Components

#1: Antibody homo-specific diabody heavy chain


Mass: 13244.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#2: Antibody homo-specific diabody light chain


Mass: 13640.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 3.98 Å3/Da / Density % sol: 69.07 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 2.3 M Sodium acetate, 5% glycerol

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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: Apr 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 18614 / % possible obs: 99.9 % / Redundancy: 17.4 % / Net I/σ(I): 24.2
Reflection shellResolution: 2.3→2.38 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: 2.3→36.232 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 24.98
RfactorNum. reflection% reflection
Rfree0.2209 928 5 %
Rwork0.1835 --
obs0.1853 18570 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→36.232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1727 0 0 222 1949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091771
X-RAY DIFFRACTIONf_angle_d1.372408
X-RAY DIFFRACTIONf_dihedral_angle_d15.906618
X-RAY DIFFRACTIONf_chiral_restr0.089258
X-RAY DIFFRACTIONf_plane_restr0.005310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2904-2.41110.35111240.26642378X-RAY DIFFRACTION95
2.4111-2.56210.30951300.23762473X-RAY DIFFRACTION100
2.5621-2.75990.28271320.2252498X-RAY DIFFRACTION100
2.7599-3.03750.26111310.20232506X-RAY DIFFRACTION100
3.0375-3.47670.21391330.17852518X-RAY DIFFRACTION100
3.4767-4.37910.18431340.14772555X-RAY DIFFRACTION100
4.3791-36.23630.16671440.15662714X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 14.1079 Å / Origin y: -42.2497 Å / Origin z: -30.6164 Å
111213212223313233
T0.1257 Å20.0162 Å2-0.0042 Å2-0.1253 Å2-0.0584 Å2--0.2154 Å2
L0.403 °2-0.0837 °2-0.0931 °2-0.3687 °20.1534 °2--0.6036 °2
S-0.0737 Å °-0.0484 Å °-0.1968 Å °0.0411 Å °0.0217 Å °0.1561 Å °0.0207 Å °0.023 Å °0.0099 Å °
Refinement TLS groupSelection details: all

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