[English] 日本語
Yorodumi
- PDB-8wug: The Crystal Structure of JMJD2D from Biortus. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8wug
TitleThe Crystal Structure of JMJD2D from Biortus.
ComponentsLysine-specific demethylase 4D
KeywordsOXIDOREDUCTASE / Chromatin regulator / Dioxygenase / Transcription / Transcription regulation / Iron / Metal-binding / Zinc
Function / homology
Function and homology information


immune system process / plasma membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / T cell receptor beta variable 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Guo, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of JMJD2D from Biortus.
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Guo, S.
History
DepositionOct 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lysine-specific demethylase 4D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0378
Polymers39,4921
Non-polymers5457
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-15 kcal/mol
Surface area15120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.340, 71.340, 150.873
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-810-

HOH

21A-828-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Lysine-specific demethylase 4D


Mass: 39491.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4D / Production host: Escherichia coli (E. coli) / References: UniProt: Q6B0I6

-
Non-polymers , 6 types, 428 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES, NaOH pH 7.5, 2% PEG 400, 2M Ammonium Sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.7→47.89 Å / Num. obs: 40301 / % possible obs: 92 % / Redundancy: 15.9 % / Rmerge(I) obs: 0.029 / Net I/σ(I): 60.6
Reflection shellResolution: 1.7→1.74 Å / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 13.4 / Num. unique obs: 2235

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→47.887 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.188 / WRfactor Rwork: 0.161 / SU B: 1.543 / SU ML: 0.053 / Average fsc free: 0.9766 / Average fsc work: 0.9837 / Cross valid method: FREE R-VALUE / ESU R: 0.101 / ESU R Free: 0.096
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1876 2006 4.988 %
Rwork0.1612 38214 -
all0.163 --
obs-40220 92.009 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.554 Å2
Baniso -1Baniso -2Baniso -3
1-0.597 Å2-0 Å2-0 Å2
2--0.597 Å2-0 Å2
3----1.193 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2687 0 28 421 3136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122849
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162491
X-RAY DIFFRACTIONr_angle_refined_deg1.1311.6613856
X-RAY DIFFRACTIONr_angle_other_deg0.3991.5655825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4765343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.231518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1910469
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.82110144
X-RAY DIFFRACTIONr_chiral_restr0.0590.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023241
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02617
X-RAY DIFFRACTIONr_nbd_refined0.2110.2590
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.22371
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21351
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21356
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2285
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1170.211
X-RAY DIFFRACTIONr_nbd_other0.1070.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1690.240
X-RAY DIFFRACTIONr_mcbond_it1.1842.0061333
X-RAY DIFFRACTIONr_mcbond_other1.1842.0061333
X-RAY DIFFRACTIONr_mcangle_it1.8963.0051668
X-RAY DIFFRACTIONr_mcangle_other1.8963.0071669
X-RAY DIFFRACTIONr_scbond_it1.8892.2911516
X-RAY DIFFRACTIONr_scbond_other1.8882.2931517
X-RAY DIFFRACTIONr_scangle_it2.9583.3272181
X-RAY DIFFRACTIONr_scangle_other2.9583.3292182
X-RAY DIFFRACTIONr_lrange_it5.69530.3983455
X-RAY DIFFRACTIONr_lrange_other5.3825.8493322
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.7-1.7440.2241380.1729960.17331700.9730.98298.86430.17
1.744-1.7920.2051460.17129330.17330790.9740.9821000.171
1.792-1.8440.2061710.16928170.17129880.9750.9831000.169
1.844-1.90.199760.17116790.17229390.9760.98359.71420.171
1.9-1.9630.204850.1616600.16128470.9740.98461.29260.16
1.963-2.0310.1611370.16226160.16227530.9830.9841000.162
2.031-2.1080.1821370.15825230.1626600.9790.9841000.158
2.108-2.1940.1831210.15624410.15725620.9810.9861000.156
2.194-2.2910.1821480.15723240.15824720.9790.9851000.157
2.291-2.4030.2011100.15622510.15823610.9740.9841000.156
2.403-2.5320.2021210.15821300.1622510.9760.9841000.158
2.532-2.6850.24830.16314200.16721330.9640.98370.46410.163
2.685-2.870.1711010.15718940.15820240.9760.98498.56720.157
2.87-3.0990.1791040.16317930.16418980.9790.98399.94730.163
3.099-3.3940.207740.16116770.16317510.9730.9841000.161
3.394-3.7920.194520.16311200.16415880.9730.98473.80350.163
3.792-4.3740.159680.14312580.14414150.9850.98893.71030.143
4.374-5.3460.16520.14411830.14412350.9910.9881000.144
5.346-7.5130.232500.1989250.29760.9720.9899.89750.198
7.513-47.8870.159320.25740.1986080.9820.97199.67110.2

+
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