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- PDB-5yzw: Crystal structure of p204 HINb domain -

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Basic information

Entry
Database: PDB / ID: 5yzw
TitleCrystal structure of p204 HINb domain
ComponentsIfi204
KeywordsIMMUNE SYSTEM / Interferon inducible gene 204 / IFI204 / DNA sensor / PYHIN family
Function / homology
Function and homology information


cellular response to interferon-alpha / nuclear inclusion body / inner ear development / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / cellular response to interferon-beta / positive regulation of osteoblast differentiation / activation of innate immune response / Neutrophil degranulation / transcription coregulator activity / response to bacterium ...cellular response to interferon-alpha / nuclear inclusion body / inner ear development / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / cellular response to interferon-beta / positive regulation of osteoblast differentiation / activation of innate immune response / Neutrophil degranulation / transcription coregulator activity / response to bacterium / double-stranded DNA binding / nuclear speck / innate immune response / nucleolus / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
HIN-200/IF120x / HIN-200 family / HIN-200/IF120x domain / HIN-200 A and B domains profile. / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Death-like domain superfamily / Nucleic acid-binding proteins ...HIN-200/IF120x / HIN-200 family / HIN-200/IF120x domain / HIN-200 A and B domains profile. / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Death-like domain superfamily / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Ifi204 / Interferon-activable protein 204
Similarity search - Component
Biological speciesMus musculus domesticus (western European house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsJin, T.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structural mechanism of DNA recognition by the p204 HIN domain.
Authors: Fan, X. / Jiang, J. / Zhao, D. / Chen, F. / Ma, H. / Smith, P. / Unterholzner, L. / Xiao, T.S. / Jin, T.
History
DepositionDec 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rrim_I_all / _reflns_shell.pdbx_Rrim_I_all
Revision 1.2Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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: Ifi204
B: Ifi204


Theoretical massNumber of molelcules
Total (without water)45,7762
Polymers45,7762
Non-polymers00
Water2,414134
1
A: Ifi204


Theoretical massNumber of molelcules
Total (without water)22,8881
Polymers22,8881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ifi204


Theoretical massNumber of molelcules
Total (without water)22,8881
Polymers22,8881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.720, 99.720, 107.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Ifi204


Mass: 22888.189 Da / Num. of mol.: 2 / Fragment: UNP residues 448-640
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus domesticus (western European house mouse)
Gene: Ifi204 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Z3MI45, UniProt: P0DOV2*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 3.49 Å3/Da / Density % sol: 64.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 20% PEG300, 100 mM Bicine pH 8.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 41767 / % possible obs: 99.6 % / Redundancy: 10.7 % / CC1/2: 0.999 / Rrim(I) all: 0.074 / Net I/σ(I): 18.35
Reflection shellResolution: 2→2.12 Å / Redundancy: 10.85 % / Num. unique obs: 6643 / CC1/2: 0.841 / Rrim(I) all: 1.366 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(dev_2481: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RLO

3rlo


Resolution: 2.001→33.607 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.24
RfactorNum. reflection% reflection
Rfree0.2544 2066 4.95 %
Rwork0.2045 --
obs0.2069 41703 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.001→33.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3096 0 0 134 3230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073200
X-RAY DIFFRACTIONf_angle_d0.8444331
X-RAY DIFFRACTIONf_dihedral_angle_d3.0922662
X-RAY DIFFRACTIONf_chiral_restr0.06483
X-RAY DIFFRACTIONf_plane_restr0.005554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0011-2.04770.32211250.31622567X-RAY DIFFRACTION99
2.0477-2.09890.33451430.30252606X-RAY DIFFRACTION100
2.0989-2.15560.311680.27192598X-RAY DIFFRACTION100
2.1556-2.2190.26981290.26162645X-RAY DIFFRACTION100
2.219-2.29060.40051160.31142587X-RAY DIFFRACTION99
2.2906-2.37250.28721550.25132618X-RAY DIFFRACTION100
2.3725-2.46740.26391290.24112623X-RAY DIFFRACTION100
2.4674-2.57970.30591420.252636X-RAY DIFFRACTION100
2.5797-2.71560.28041250.24312678X-RAY DIFFRACTION100
2.7156-2.88570.26151390.22732630X-RAY DIFFRACTION100
2.8857-3.10840.28821380.24022665X-RAY DIFFRACTION100
3.1084-3.42090.30771700.22692634X-RAY DIFFRACTION100
3.4209-3.91530.23541330.19252687X-RAY DIFFRACTION100
3.9153-4.93030.19821220.14982727X-RAY DIFFRACTION100
4.9303-33.61210.21571320.17632736X-RAY DIFFRACTION97
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)
11.2730.90620.26261.32680.51880.4819-0.06650.10880.2031-0.71930.04440.05820.2740.0275-0.00550.5253-0.11630.03680.2998-0.01960.3992-36.64666.9228-4.9379
21.05-0.47570.88912.06761.3441.73070.1647-0.4943-0.31660.2822-0.37030.04510.17630.1222-0.00050.4801-0.15340.0550.3198-0.00530.3738-38.43161.07885.3514
30.20550.45950.23670.55340.39340.2261-0.0717-0.2075-0.1196-0.33480.06570.13750.3179-0.004-0.00010.6304-0.1540.12380.3595-0.03920.456-36.7238-5.2304-1.5756
40.2023-0.3433-0.07611.1578-0.51320.9239-0.0450.17380.0317-0.5843-0.09290.2846-0.1973-0.4915-0.00590.5018-0.12080.00040.3431-0.00980.4089-40.98815.794-2.9351
51.93480.5266-0.5971.2384-0.85631.0219-0.24070.1462-0.3588-0.02880.2047-0.58330.80480.5873-0.020.4721-0.03150.01750.4392-0.0530.5442-24.26125.08871.0483
60.7024-0.24740.05410.80550.32290.83110.1472-0.1930.25491.3289-0.0598-0.48840.4290.4507-0.04420.9648-0.062-0.15160.55-0.02260.5154-29.93796.833121.9227
71.0739-0.4226-0.7153.099-0.3461.11660.2264-2.030.35572.2189-0.4635-0.68331.12051.07790.03591.2288-0.1043-0.09320.7002-0.02830.4346-30.2545.865226.318
80.99250.2185-0.14080.2064-0.16890.37530.269-0.4980.0251.0582-0.3175-0.00330.8962-0.214-0.06011.0041-0.1729-0.08370.46380.05070.3806-33.62650.692820.8764
90.6982-0.50670.45370.190.14060.14950.0807-0.4081-0.01511.3127-0.12510.1961.0786-0.0834-0.00120.8317-0.06150.01260.4547-0.03720.4112-34.46436.903620.4202
101.9248-1.3478-0.69643.92870.54140.94160.0384-0.15420.0641-0.55890.028-0.2086-0.12420.16340.00170.6097-0.20390.02570.2899-0.02930.354-32.949325.6125-7.7521
110.7068-0.89980.33461.97580.56740.7530.31060.5432-0.0675-0.688-0.18820.0569-0.18510.2776-0.00030.6905-0.0349-0.00040.4452-0.01020.4943-37.424816.8229-17.939
123.60280.15930.18111.49841.37720.61460.1615-0.07750.3816-0.2915-0.28060.4303-0.3011-0.08930.00010.717-0.0204-0.16440.3838-0.04360.6601-54.720130.8492-13.7239
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 425 through 440 )
2X-RAY DIFFRACTION2chain 'A' and (resid 441 through 470 )
3X-RAY DIFFRACTION3chain 'A' and (resid 471 through 483 )
4X-RAY DIFFRACTION4chain 'A' and (resid 484 through 504 )
5X-RAY DIFFRACTION5chain 'A' and (resid 505 through 535 )
6X-RAY DIFFRACTION6chain 'A' and (resid 536 through 554 )
7X-RAY DIFFRACTION7chain 'A' and (resid 555 through 573 )
8X-RAY DIFFRACTION8chain 'A' and (resid 574 through 597 )
9X-RAY DIFFRACTION9chain 'A' and (resid 598 through 615 )
10X-RAY DIFFRACTION10chain 'B' and (resid 423 through 504 )
11X-RAY DIFFRACTION11chain 'B' and (resid 505 through 535 )
12X-RAY DIFFRACTION12chain 'B' and (resid 536 through 615 )

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