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- PDB-1b5l: OVINE INTERFERON TAU -

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Basic information

Entry
Database: PDB / ID: 1b5l
TitleOVINE INTERFERON TAU
ComponentsINTERFERON TAU
KeywordsCYTOKINE
Function / homology
Function and homology information


cytokine receptor binding / cytokine activity / female pregnancy / hormone activity / defense response to virus / extracellular space
Similarity search - Function
Interferon alpha, beta and delta family signature. / Interferon alpha, beta and delta. / Interferon alpha/beta/delta / Interferon alpha/beta domain / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPichia pastoris (fungus)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.1 Å
AuthorsRadhakrishnan, R. / Walter, L.J. / Subramaniam, P.S. / Johnson, H.J. / Walter, M.R.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of ovine interferon-tau at 2.1 A resolution.
Authors: Radhakrishnan, R. / Walter, L.J. / Subramaniam, P.S. / Johnson, H.M. / Walter, M.R.
History
DepositionJan 7, 1999Processing site: BNL
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTERFERON TAU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1283
Polymers19,9361
Non-polymers1922
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.300, 45.600, 75.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein INTERFERON TAU


Mass: 19935.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pichia pastoris (fungus) / Production host: Pichia pastoris (fungus) / References: UniProt: P56828
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.71 Å3/Da / Density % sol: 28 %
Crystal growpH: 4.8 / Details: pH 4.8
Crystal
*PLUS
Density % sol: 27 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
20.8 M1reservoirLi2SO4
3100 mMcitrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceWavelength: 1.5418
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→15 Å / Num. obs: 8216 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.043

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Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: MIR / Resolution: 2.1→15 Å / Data cutoff high rms absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0.1 / Stereochemistry target values: MLF
Details: SIDE-CHAIN ATOMS OF RESIDUES 115, 125 AND 161 WERE NOT OBSERVED IN ELECTRON DENSITY MAPS.
RfactorNum. reflection% reflection
Rfree0.25 865 10 %
Rwork0.214 --
obs0.214 8066 96.4 %
Solvent computationSolvent model: FLAT MODEL / Bsol: 83.04 Å2 / ksol: 0.382 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.513 Å20 Å20 Å2
2--5.113 Å20 Å2
3---3.4 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1237 0 2 87 1326
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARAM.WAT
X-RAY DIFFRACTION2PARAM.SO4
Refinement
*PLUS
Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS

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