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- PDB-5gs2: Crystal structure of diabody complex with repebody and MBP -

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Basic information

Entry
Database: PDB / ID: 5gs2
TitleCrystal structure of diabody complex with repebody and MBP
Components
  • Maltose-binding periplasmic protein
  • anti-MBP
  • anti-repebody
  • repebody
KeywordsSUGAR BINDING PROTEIN/IMMUNE SYSTEM / diabody / antibody fragment / complex / SUGAR BINDING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / 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 ...Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / 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 / Alpha Beta
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.592 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein
D: anti-repebody
H: anti-MBP
B: repebody


Theoretical massNumber of molelcules
Total (without water)121,8064
Polymers121,8064
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)278.835, 278.835, 132.322
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 40366.621 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 27-393 / Mutation: R367N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: malE, b4034, JW3994 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9
#2: Antibody anti-repebody


Mass: 25138.881 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Antibody anti-MBP


Mass: 25901.592 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Protein repebody


Mass: 30398.408 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
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: 4.08 Å3/Da / Density % sol: 69.88 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: 0.1 M Sodium acetate pH 4.2, 2 M Ammonium sulfate

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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: Nov 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 22895 / % possible obs: 100 % / Redundancy: 10.2 % / Net I/σ(I): 20.7
Reflection shellResolution: 3.6→3.73 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: 3PGF, 3RFJ, 4J8R

3pgf

3rfj

4j8r


Resolution: 3.592→44.107 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2776 1999 8.74 %
Rwork0.2168 --
obs0.2221 22880 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.592→44.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8461 0 0 0 8461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0138746
X-RAY DIFFRACTIONf_angle_d1.68111901
X-RAY DIFFRACTIONf_dihedral_angle_d13.0675221
X-RAY DIFFRACTIONf_chiral_restr0.0911327
X-RAY DIFFRACTIONf_plane_restr0.011518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5923-3.68210.32941310.2581377X-RAY DIFFRACTION93
3.6821-3.78160.28961450.25141495X-RAY DIFFRACTION100
3.7816-3.89280.35611410.26441476X-RAY DIFFRACTION100
3.8928-4.01840.32851420.2521488X-RAY DIFFRACTION100
4.0184-4.16190.35691430.23771502X-RAY DIFFRACTION100
4.1619-4.32840.27341420.21531468X-RAY DIFFRACTION100
4.3284-4.52520.26771430.19061503X-RAY DIFFRACTION100
4.5252-4.76350.23271440.19321498X-RAY DIFFRACTION100
4.7635-5.06150.21391430.17281504X-RAY DIFFRACTION100
5.0615-5.45170.23831420.18931476X-RAY DIFFRACTION100
5.4517-5.99910.27341450.22231514X-RAY DIFFRACTION100
5.9991-6.86440.2871440.23491509X-RAY DIFFRACTION100
6.8644-8.63780.30161460.22721516X-RAY DIFFRACTION100
8.6378-44.11060.25821480.20691555X-RAY DIFFRACTION99

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