[English] 日本語
Yorodumi
- PDB-8idx: Structure of p205 HIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8idx
TitleStructure of p205 HIN
ComponentsInterferon-activable protein 205-B
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


cellular response to interferon-beta / Neutrophil degranulation / activation of innate immune response / nuclear periphery / nuclear speck / nucleus
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, OB-fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Interferon-activable protein 211
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLi, Y.L. / Jin, T.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: to Be published
Title: Structure of p205 HIN
Authors: Li, Y.L. / Jin, T.C.
History
DepositionFeb 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Interferon-activable protein 205-B
B: Interferon-activable protein 205-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,49134
Polymers49,1082
Non-polymers2,38332
Water3,765209
1
A: Interferon-activable protein 205-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,80319
Polymers24,5541
Non-polymers1,24918
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Interferon-activable protein 205-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,68715
Polymers24,5541
Non-polymers1,13314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.638, 51.121, 56.578
Angle α, β, γ (deg.)103.15, 105.17, 108.29
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Interferon-activable protein 205-B / Ifi-205-B / Interferon-inducible protein p205-B / Myeloid cell nuclear differentiation antigen / Protein D3


Mass: 24553.928 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mnda, Ifi205b / Plasmid: PET30a / Details (production host): MBP tag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DOV1
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1 M Sodium chloride, 0.1 M BICINE pH 9.0, 25% v/v Polyethylene glycol monomethyl ether 550

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.75→29.546 Å / Num. obs: 158200 / % possible obs: 95.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 28.28 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.02271 / Rpim(I) all: 0.01421 / Rrim(I) all: 0.02688 / Net I/σ(I): 28.96
Reflection shellResolution: 1.75→1.813 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.2504 / Num. unique obs: 15198 / CC1/2: 0.969 / CC star: 0.992 / Rrim(I) all: 0.2991 / % possible all: 94.55

-
Processing

Software
NameVersionClassification
PHENIX(1.15_3459: ???)refinement
XDSdata scaling
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→29.546 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 25.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1988 2277 5.01 %
Rwork0.1725 --
obs0.1738 45448 95.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.546 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3066 0 155 209 3430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063257
X-RAY DIFFRACTIONf_angle_d0.7654323
X-RAY DIFFRACTIONf_dihedral_angle_d6.9071930
X-RAY DIFFRACTIONf_chiral_restr0.056478
X-RAY DIFFRACTIONf_plane_restr0.005538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7502-1.78830.30881400.23862609X-RAY DIFFRACTION93
1.7883-1.82990.30461480.22642685X-RAY DIFFRACTION95
1.8299-1.87560.24921340.20612669X-RAY DIFFRACTION95
1.8756-1.92630.28321400.21222629X-RAY DIFFRACTION95
1.9263-1.9830.20491460.19112691X-RAY DIFFRACTION96
1.983-2.0470.26331440.19352713X-RAY DIFFRACTION96
2.047-2.12010.23171350.2042673X-RAY DIFFRACTION95
2.1201-2.2050.22411480.19022710X-RAY DIFFRACTION96
2.205-2.30530.22561340.19782705X-RAY DIFFRACTION96
2.3053-2.42680.2491490.19892707X-RAY DIFFRACTION97
2.4268-2.57880.21441400.19322743X-RAY DIFFRACTION97
2.5788-2.77770.21741390.18682713X-RAY DIFFRACTION97
2.7777-3.0570.22941480.18112736X-RAY DIFFRACTION97
3.057-3.49880.21631450.17192731X-RAY DIFFRACTION97
3.4988-4.40570.15911450.14592727X-RAY DIFFRACTION97
4.4057-29.5460.15351420.14892730X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 7.2558 Å / Origin y: -7.9458 Å / Origin z: 9.4848 Å
111213212223313233
T0.2389 Å2-0.0702 Å20.0138 Å2-0.2609 Å2-0.0056 Å2--0.233 Å2
L0.2932 °2-0.2757 °2-0.0492 °2-2.8463 °20.7125 °2--0.9372 °2
S-0.037 Å °0.0193 Å °0.0286 Å °0.0238 Å °0.0912 Å °0.0281 Å °-0.0652 Å °0.0594 Å °-0.0504 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more