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- PDB-5zny: Structure of mDR3_DD-C363G with MBP tag -

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Basic information

Entry
Database: PDB / ID: 5zny
TitleStructure of mDR3_DD-C363G with MBP tag
ComponentsMaltose-binding periplasmic protein,Tumor necrosis factor receptor superfamily, member 25
KeywordsAPOPTOSIS / TNFRSF25 / NF-kappa B / TRADD
Function / homology
Function and homology information


TNFs bind their physiological receptors / 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 ...TNFs bind their physiological receptors / 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 / apoptotic process / DNA damage response / signal transduction / membrane / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 25 / Tumor necrosis factor receptor 25, N-terminal / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain ...Tumour necrosis factor receptor 25 / Tumor necrosis factor receptor 25, N-terminal / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / 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 / Death-like domain superfamily
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily, member 25 / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsYin, X. / Jin, T.
CitationJournal: Febs J. / Year: 2019
Title: Crystal structure and activation mechanism of DR3 death domain.
Authors: Yin, X. / Li, W. / Ma, H. / Zeng, W. / Peng, C. / Li, Y. / Liu, M. / Chen, Q. / Zhou, R. / Jin, T.
History
DepositionApr 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Dec 4, 2019Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein,Tumor necrosis factor receptor superfamily, member 25
B: Maltose-binding periplasmic protein,Tumor necrosis factor receptor superfamily, member 25
C: Maltose-binding periplasmic protein,Tumor necrosis factor receptor superfamily, member 25
D: Maltose-binding periplasmic protein,Tumor necrosis factor receptor superfamily, member 25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,89031
Polymers205,2974
Non-polymers2,59427
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13070 Å2
ΔGint-395 kcal/mol
Surface area71670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.320, 145.150, 178.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Maltose-binding periplasmic protein,Tumor necrosis factor receptor superfamily, member 25 / MBP / MMBP / Maltodextrin-binding protein / TNFRSF25 / Tumor necrosis factor receptor superfamily / ...MBP / MMBP / Maltodextrin-binding protein / TNFRSF25 / Tumor necrosis factor receptor superfamily / member 25 / isoform CRA_b


Mass: 51324.188 Da / Num. of mol.: 4
Mutation: D108A,K109A,E198A,N199A,K265A,E385A,K388A,D389A,I387V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Mus musculus (house mouse)
Strain: K12 / Gene: malE, b4034, JW3994, Tnfrsf25, mCG_4090 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: B1AWN9
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.85 Å3/Da / Density % sol: 56.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 2.2 M ammonium sulfate, 0.1 M MES pH 5.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.74→47.79 Å / Num. obs: 62248 / % possible obs: 99.8 % / Redundancy: 6.44 % / CC1/2: 0.999 / Net I/σ(I): 18.29
Reflection shellResolution: 2.74→2.91 Å / Num. unique obs: 62030 / CC1/2: 0.744

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Processing

Software
NameVersionClassification
PHENIX1.12-2829refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OMP

1omp


Resolution: 2.74→47.78 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2481 3112 5 %random selection
Rwork0.2097 ---
obs-62194 99.73 %-
Refinement stepCycle: LAST / Resolution: 2.74→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13959 0 135 4 14098
LS refinement shellResolution: 2.74→2.838 Å
Refinement TLS params.Method: refined / Origin x: 135.7524 Å / Origin y: 3.6678 Å / Origin z: 43.986 Å
111213212223313233
T0.5131 Å20.0095 Å2-0.0253 Å2-0.505 Å20.0035 Å2--0.4371 Å2
L0.1061 °20.0663 °2-0.0039 °2-0.4809 °20.0753 °2--0.3764 °2
S-0.0306 Å °-0.0032 Å °0.0293 Å °-0.0277 Å °-0.0087 Å °-0.0068 Å °0.0069 Å °-0.0745 Å °0.0254 Å °
Refinement TLS groupSelection details: all

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