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- PDB-4g1t: Crystal structure of interferon-stimulated gene 54 -

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Basic information

Entry
Database: PDB / ID: 4g1t
TitleCrystal structure of interferon-stimulated gene 54
ComponentsInterferon-induced protein with tetratricopeptide repeats 2
KeywordsANTIVIRAL PROTEIN / ISG / all alpha helix / antivirus
Function / homology
Function and homology information


apoptotic mitochondrial changes / negative regulation of protein binding / antiviral innate immune response / response to virus / Interferon alpha/beta signaling / defense response to virus / positive regulation of apoptotic process / endoplasmic reticulum / RNA binding / cytosol / cytoplasm
Similarity search - Function
Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Interferon-induced protein with tetratricopeptide repeats 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsYang, Z. / Liang, H. / Zhou, Q. / Li, Y. / Chen, H. / Ye, W. / Chen, D. / Fleming, J. / Shu, H. / Liu, Y.
CitationJournal: Cell Res. / Year: 2012
Title: Crystal structure of ISG54 reveals a novel RNA binding structure and potential functional mechanisms.
Authors: Yang, Z. / Liang, H. / Zhou, Q. / Li, Y. / Chen, H. / Ye, W. / Chen, D. / Fleming, J. / Shu, H. / Liu, Y.
History
DepositionJul 11, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interferon-induced protein with tetratricopeptide repeats 2
B: Interferon-induced protein with tetratricopeptide repeats 2


Theoretical massNumber of molelcules
Total (without water)109,4602
Polymers109,4602
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8290 Å2
ΔGint-33 kcal/mol
Surface area41550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.023, 95.207, 155.900
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-induced protein with tetratricopeptide repeats 2 / IFIT-2 / ISG-54 K / Interferon-induced 54 kDa protein / IFI-54K


Mass: 54730.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFIT2, G10P2, IFI54 / Production host: Escherichia coli (E. coli) / References: UniProt: P09913
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNATURAL VALIANT D -> E AT THIS POSITION

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL17U10.979
SYNCHROTRONPhoton Factory BL-5A20.978
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDOct 7, 2010
ADSC QUANTUM 3152CCDJun 6, 2010
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.9781
ReflectionResolution: 2.8→40 Å / Num. all: 29758 / Num. obs: 29706 / % possible obs: 99 % / Observed criterion σ(F): 4.4 / Observed criterion σ(I): 121.7 / Biso Wilson estimate: 63.88 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.8-2.851,287.1
2.85-2.91,294.5
2.9-2.961,298.2
2.96-3.021,299.6
3.02-3.081,2100
3.08-3.151,2100
3.15-3.231,2100
3.23-3.321,2100
3.32-3.421,2100
3.42-3.531,299.9
3.53-3.651,2100
3.65-3.81,2100
3.8-3.971,2100
3.97-4.181,2100
4.18-4.441,2100
4.44-4.791,2100
4.79-5.271,2100
5.27-6.031,299.9
6.03-7.591,2100
7.59-501,298.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→39.572 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7453 / SU ML: 0.41 / σ(F): 0 / Phase error: 31.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2866 1505 5.07 %
Rwork0.2342 28187 -
obs0.2369 29692 98.83 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.97 Å2 / ksol: 0.301 e/Å3
Displacement parametersBiso max: 172.71 Å2 / Biso mean: 70.293 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-1.4558 Å2-0 Å20 Å2
2---13.7221 Å2-0 Å2
3---12.2664 Å2
Refinement stepCycle: LAST / Resolution: 2.8→39.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6847 0 0 23 6870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016920
X-RAY DIFFRACTIONf_angle_d1.2429305
X-RAY DIFFRACTIONf_chiral_restr0.0771007
X-RAY DIFFRACTIONf_plane_restr0.0051197
X-RAY DIFFRACTIONf_dihedral_angle_d18.032606
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8002-2.89060.4291240.31932297242189
2.8906-2.99380.31831230.31962507263098
2.9938-3.11370.34431360.301925522688100
3.1137-3.25530.38771480.279725342682100
3.2553-3.42680.3331430.265525652708100
3.4268-3.64140.3171090.254726082717100
3.6414-3.92230.31361220.218425732695100
3.9223-4.31660.22331420.202525952737100
4.3166-4.94020.25661530.193925952748100
4.9402-6.22030.29791540.276926332787100
6.2203-39.57590.23961510.19582728287999

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