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- PDB-7e0e: Crystal structure of mouse interferon alpha2 at 2.1 angstrom reso... -

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Basic information

Entry
Database: PDB / ID: 7e0e
TitleCrystal structure of mouse interferon alpha2 at 2.1 angstrom resolution
ComponentsInterferon alpha-2Interferon type I
KeywordsCYTOKINE / Interferon / Immune system / Mouse
Function / homology
Function and homology information


cytokine receptor binding / cytokine 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 / Four-helical cytokine-like, core
Similarity search - Domain/homology
PHOSPHATE ION / Interferon alpha-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.102 Å
AuthorsWatanabe, H. / Yabe-Wada, T. / Unno, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP19K06550 Japan
CitationJournal: J.Biochem. / Year: 2021
Title: Detailed structure of mouse interferon alpha 2 and its interaction with Sortilin.
Authors: Watanabe, H. / Yabe-Wada, T. / Onai, N. / Unno, M.
History
DepositionJan 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 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: Interferon alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8516
Polymers19,3871
Non-polymers4635
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-8 kcal/mol
Surface area8420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.733, 42.733, 180.695
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-301-

GOL

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Components

#1: Protein Interferon alpha-2 / Interferon type I


Mass: 19387.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ifna2 / Production host: Escherichia coli (E. coli) / References: UniProt: B1AYH7
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.13 Å3/Da / Density % sol: 42.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: MES, PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→29.803 Å / Num. obs: 10532 / % possible obs: 100 % / Redundancy: 12.35 % / Biso Wilson estimate: 37.87 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.083 / Χ2: 1.1 / Net I/σ(I): 26.01 / Num. measured all: 130066
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.2312.8080.654.121185165416540.9630.677100
2.23-2.3812.5770.3826.8519582155815570.9840.39899.9
2.38-2.5712.3510.22810.8517785144014400.9950.238100
2.57-2.8212.9680.16615.4917481134813480.9960.173100
2.82-3.1512.3550.10224.8515209123112310.9980.106100
3.15-3.6312.4530.06238.7713661109710970.9990.065100
3.63-4.4411.9730.03961.54114469579560.9990.04199.9
4.44-6.2511.5650.03365.32888276876810.035100
6.25-29.80310.0520.02178.63483548248110.02399.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ITF

1itf


Resolution: 2.102→29.803 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2153 526 5 %
Rwork0.1882 9986 -
obs0.1896 10512 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.81 Å2 / Biso mean: 50.0035 Å2 / Biso min: 20.09 Å2
Refinement stepCycle: final / Resolution: 2.102→29.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1218 0 29 93 1340
Biso mean--82.1 48.63 -
Num. residues----149
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.102-2.3130.25091270.20162405
2.313-2.64750.2461290.1972453
2.6475-3.33490.20621300.19922472
3.3349-29.8030.20471400.17822656
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.62252.2203-0.1944.8246-0.5575.46890.08960.452-0.01670.04640.1110.27920.2784-0.6412-0.15460.3056-0.0143-0.0090.3307-0.02340.126110.655528.423851.5918
25.08256.90932.42259.51223.30066.2055-1.64052.6150.6007-1.82691.51662.58911.3147-0.02560.0991.3028-0.1953-0.45561.3076-0.2991.508312.22916.957548.4689
34.81795.83493.73958.30764.87043.03920.5575-0.268-1.05910.811-0.1308-0.79411.1051-0.2832-0.46950.4967-0.0296-0.03850.21860.03280.39998.572516.89460.7735
44.92252.82861.12527.03673.185.59260.0172-0.0560.13490.29190.00540.37490.2875-0.77110.09820.26660.01070.05570.35780.00670.18143.441828.514962.455
53.19760.43870.78254.18790.19130.88660.18950.0731.0304-0.6755-0.147-0.0928-0.19470.17830.07881.6502-0.36340.45660.3727-0.2921.017515.29427.397155.2861
63.53751.46950.77863.11680.38074.29650.09310.0836-0.57680.02040.1211-0.22310.4754-0.1294-0.15720.2993-0.0038-0.05290.2263-0.01640.2516.618124.081957.5502
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 42 )A4 - 42
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 49 )A43 - 49
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 68 )A50 - 68
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 98 )A69 - 98
5X-RAY DIFFRACTION5chain 'A' and (resid 99 through 112 )A99 - 112
6X-RAY DIFFRACTION6chain 'A' and (resid 113 through 161 )A113 - 161

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