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- PDB-8hcs: zebrafish IRF-11 DBD -

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Basic information

Entry
Database: PDB / ID: 8hcs
Titlezebrafish IRF-11 DBD
ComponentsInterferon regulatory factor
KeywordsDNA BINDING PROTEIN / zebrafish / IRF / DBD
Function / homology
Function and homology information


immune system process / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Interferon regulatory factor-1/2 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor / Interferon regulatory factor DNA-binding domain / IRF tryptophan pentad repeat DNA-binding domain profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Interferon regulatory factor
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsWang, Z.X. / Zhang, Y.A. / Ouyang, S.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31725026; 82225028; 82172287 China
CitationJournal: J Immunol. / Year: 2024
Title: Crystal Structures of DNA-bound Fish IRF10 and IRF11 Reveal the Determinants of IFN Regulation.
Authors: Wang, Z.X. / Liu, B. / Xie, H. / Liu, X. / Li, X. / Shi, F. / Ouyang, S. / Zhang, Y.A.
History
DepositionNov 3, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 4, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interferon regulatory factor


Theoretical massNumber of molelcules
Total (without water)13,2721
Polymers13,2721
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.324, 101.324, 101.324
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332
Space group name HallP4acd2ab3
Symmetry operation#1: x,y,z
#2: x+3/4,-z+3/4,y+1/4
#3: x+1/4,z+3/4,-y+3/4
#4: z+1/4,y+3/4,-x+3/4
#5: -z+3/4,y+1/4,x+3/4
#6: -y+3/4,x+1/4,z+3/4
#7: y+3/4,-x+3/4,z+1/4
#8: z,x,y
#9: y,z,x
#10: -y+1/2,-z,x+1/2
#11: z+1/2,-x+1/2,-y
#12: -y,z+1/2,-x+1/2
#13: -z+1/2,-x,y+1/2
#14: -z,x+1/2,-y+1/2
#15: y+1/2,-z+1/2,-x
#16: x+1/2,-y+1/2,-z
#17: -x,y+1/2,-z+1/2
#18: -x+1/2,-y,z+1/2
#19: y+1/4,x+3/4,-z+3/4
#20: -y+1/4,-x+1/4,-z+1/4
#21: z+3/4,-y+3/4,x+1/4
#22: -z+1/4,-y+1/4,-x+1/4
#23: -x+3/4,z+1/4,y+3/4
#24: -x+1/4,-z+1/4,-y+1/4

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Components

#1: Protein Interferon regulatory factor


Mass: 13272.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: IRF11, irf1, zgc:136945, irf1a / Production host: Escherichia coli (E. coli) / References: UniProt: Q1RLP9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.45 Å3/Da / Density % sol: 64.3 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 1.26 M sodium phosphate monobasic, 0.14 M potassium phosphate dibasic, pH 5.6

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Data collection

DiffractionMean temperature: 298.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2020
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.55→24.57 Å / Num. obs: 8495 / % possible obs: 90.15 % / Redundancy: 2 % / Biso Wilson estimate: 95.93 Å2 / CC1/2: 1 / Net I/σ(I): 36.4
Reflection shellResolution: 2.55→2.65 Å / Num. unique obs: 303 / CC1/2: 0.747

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
PHENIX1.19.2_4158phasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IRF

2irf


Resolution: 2.75→24.57 Å / SU ML: 0.5488 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.6283
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2741 849 10.01 %
Rwork0.2325 7632 -
obs0.237 8481 97.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.35 Å2
Refinement stepCycle: LAST / Resolution: 2.75→24.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms765 0 0 1 766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094786
X-RAY DIFFRACTIONf_angle_d1.22521064
X-RAY DIFFRACTIONf_chiral_restr0.0643109
X-RAY DIFFRACTIONf_plane_restr0.0098135
X-RAY DIFFRACTIONf_dihedral_angle_d6.291499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.920.36851480.36121323X-RAY DIFFRACTION100
2.92-3.150.49411500.36641282X-RAY DIFFRACTION100
3.15-3.460.35071300.32191219X-RAY DIFFRACTION92.59
3.47-3.960.28821330.25051176X-RAY DIFFRACTION89.72
3.97-4.990.22091480.20651312X-RAY DIFFRACTION100

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