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- PDB-7dov: The crystal structure of zebrafish tumor necrosis factor alpha -

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Basic information

Entry
Database: PDB / ID: 7dov
TitleThe crystal structure of zebrafish tumor necrosis factor alpha
ComponentsLymphotoxin-alpha
KeywordsCYTOKINE / TNF alpha / Danio rerio / Zebrafish
Function / homology
Function and homology information


fin regeneration / regeneration / intestinal epithelial structure maintenance / response to arsenic-containing substance / tumor necrosis factor receptor binding / response to exogenous dsRNA / liver development / response to bacterium / response to virus / response to molecule of bacterial origin ...fin regeneration / regeneration / intestinal epithelial structure maintenance / response to arsenic-containing substance / tumor necrosis factor receptor binding / response to exogenous dsRNA / liver development / response to bacterium / response to virus / response to molecule of bacterial origin / autophagy / response to lipopolysaccharide / membrane => GO:0016020 / defense response to bacterium / inflammatory response / immune response
Similarity search - Function
Lymphotoxin-alpha / Tumour necrosis factor / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumour necrosis factor-like domain superfamily
Similarity search - Domain/homology
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsDuan, Y. / Xia, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: The structure of zebrafish tumour necrosis factor alpha at 2.6 angstrom resolution
Authors: Duan, Y. / Xia, C.
History
DepositionDec 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lymphotoxin-alpha
B: Lymphotoxin-alpha
C: Lymphotoxin-alpha


Theoretical massNumber of molelcules
Total (without water)51,8203
Polymers51,8203
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-27 kcal/mol
Surface area17980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.328, 91.021, 63.396
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Lymphotoxin-alpha / tumor necrosis factor alpha / TNF-alpha / TNF-beta / Tumor necrosis factor ligand superfamily member 1


Mass: 17273.205 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: tnfa / Production host: Escherichia coli (E. coli) / References: UniProt: Q6T9C7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M DL-Malic acid pH 7.0, 12% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.59→51.31 Å / Num. obs: 15728 / % possible obs: 100 % / Redundancy: 25.1 % / Biso Wilson estimate: 36.59 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 32.3
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.852 / Num. unique obs: 1428

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Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
REFMAC7.0.077refinement
PHENIX1.19refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TSV

4tsv


Resolution: 2.59→44.27 Å / SU ML: 0.3566 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.7533
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2991 682 4.62 %
Rwork0.2181 14087 -
obs0.2217 14769 93.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.13 Å2
Refinement stepCycle: LAST / Resolution: 2.59→44.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3486 0 0 69 3555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02363573
X-RAY DIFFRACTIONf_angle_d2.63344842
X-RAY DIFFRACTIONf_chiral_restr0.1777532
X-RAY DIFFRACTIONf_plane_restr0.016630
X-RAY DIFFRACTIONf_dihedral_angle_d22.36671279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.790.37941040.28652126X-RAY DIFFRACTION72.12
2.79-3.070.33181380.27122816X-RAY DIFFRACTION95.32
3.07-3.510.31291570.23252973X-RAY DIFFRACTION99.97
3.51-4.420.31211400.19213013X-RAY DIFFRACTION99.84
4.42-44.270.24781430.19743159X-RAY DIFFRACTION99.79

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