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- PDB-5gru: Structure of mono-specific diabody -

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Basic information

Entry
Database: PDB / ID: 5gru
TitleStructure of mono-specific diabody
Components
  • (diabody proteinSingle-chain variable fragment) x 2
  • Maltose-binding periplasmic protein
KeywordsIMMUNE SYSTEM / diabody / antibody fragment
Function / homology
Function and homology information


detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.955 Å
AuthorsKim, J.H. / Song, D.H. / Youn, S.J. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein
H: diabody protein
L: diabody protein


Theoretical massNumber of molelcules
Total (without water)93,9423
Polymers93,9423
Non-polymers00
Water14,574809
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-35 kcal/mol
Surface area34080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.267, 50.823, 105.873
Angle α, β, γ (deg.)90.00, 111.28, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Maltose-binding periplasmic protein / MBP / MMBP / Maltodextrin-binding protein


Mass: 42147.621 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 27-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: malE, b4034, JW3994 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9
#2: Antibody diabody protein / Single-chain variable fragment


Mass: 26993.654 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: Antibody diabody protein / Single-chain variable fragment


Mass: 24800.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 809 / 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: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M Sodium citrate tribasic pH 5.6, 27.5% PEG 12000, 0.1 M Sodium iodide

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 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: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 70116 / % possible obs: 98.9 % / Redundancy: 3.2 % / Net I/σ(I): 14.2
Reflection shellResolution: 1.95→2.02 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: 1EZV, 3PGF

1ezv

3pgf


Resolution: 1.955→33.779 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.34
RfactorNum. reflection% reflection
Rfree0.2368 2000 3.02 %
Rwork0.1974 --
obs0.1986 66332 93.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.955→33.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6344 0 0 809 7153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086502
X-RAY DIFFRACTIONf_angle_d0.978838
X-RAY DIFFRACTIONf_dihedral_angle_d13.7193816
X-RAY DIFFRACTIONf_chiral_restr0.056959
X-RAY DIFFRACTIONf_plane_restr0.0061135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9548-2.00370.29911130.27043637X-RAY DIFFRACTION75
2.0037-2.05790.26881330.24624294X-RAY DIFFRACTION88
2.0579-2.11840.25731370.23594393X-RAY DIFFRACTION89
2.1184-2.18680.28941380.2294423X-RAY DIFFRACTION91
2.1868-2.26490.27721400.22084511X-RAY DIFFRACTION91
2.2649-2.35560.29451400.21894518X-RAY DIFFRACTION93
2.3556-2.46270.24891430.22244595X-RAY DIFFRACTION93
2.4627-2.59250.2651460.20934703X-RAY DIFFRACTION95
2.5925-2.75490.25541480.21114750X-RAY DIFFRACTION96
2.7549-2.96750.22681500.21124797X-RAY DIFFRACTION97
2.9675-3.26590.25261500.20434847X-RAY DIFFRACTION98
3.2659-3.7380.20551530.17894916X-RAY DIFFRACTION99
3.738-4.70740.19851530.15534924X-RAY DIFFRACTION98
4.7074-33.78420.20581560.1745024X-RAY DIFFRACTION98

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