[English] 日本語
Yorodumi
- PDB-7vjs: Human AlkB homolog ALKBH6 in complex with Tris and Ni -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vjs
TitleHuman AlkB homolog ALKBH6 in complex with Tris and Ni
ComponentsAlpha-ketoglutarate-dependent dioxygenase alkB homolog 6
KeywordsOXIDOREDUCTASE / ALKBH6 / alpha-ketoglutarate / oxidoreductase activity / DNA binding
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / dioxygenase activity / focal adhesion / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Alpha-ketoglutarate-dependent dioxygenase alkB homologue 6 / Alpha-ketoglutarate-dependent dioxygenase AlkB-like / 2OG-Fe(II) oxygenase superfamily / Alpha-ketoglutarate-dependent dioxygenase AlkB-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile.
Similarity search - Domain/homology
NICKEL (II) ION / Alpha-ketoglutarate-dependent dioxygenase alkB homolog 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.792 Å
AuthorsMa, L. / Chen, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Structural insights into the interactions and epigenetic functions of human nucleic acid repair protein ALKBH6.
Authors: Ma, L. / Lu, H. / Tian, Z. / Yang, M. / Ma, J. / Shang, G. / Liu, Y. / Xie, M. / Wang, G. / Wu, W. / Zhang, Z. / Dai, S. / Chen, Z.
History
DepositionSep 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 16, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6503
Polymers27,4691
Non-polymers1812
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-7 kcal/mol
Surface area10020 Å2
Unit cell
Length a, b, c (Å)46.374, 64.212, 88.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Alpha-ketoglutarate-dependent dioxygenase alkB homolog 6 / Alkylated DNA repair protein alkB homolog 6


Mass: 27469.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALKBH6, ABH6 / Production host: Komagataella pastoris (fungus)
References: UniProt: Q3KRA9, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG 8000, Tris

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 25643 / % possible obs: 99.8 % / Redundancy: 7.1 % / CC1/2: 0.994 / Net I/σ(I): 31.5
Reflection shellResolution: 1.79→1.82 Å / Num. unique obs: 2131 / CC1/2: 0.612

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3THP

3thp


Resolution: 1.792→19.724 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.192 / SU B: 2.262 / SU ML: 0.07 / Average fsc free: 0.9271 / Average fsc work: 0.9297 / Cross valid method: FREE R-VALUE / ESU R: 0.111 / ESU R Free: 0.103
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2144 1261 4.965 %
Rwork0.1969 24135 -
all0.198 --
obs-25396 99.06 %
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: 22.654 Å2
Baniso -1Baniso -2Baniso -3
1--0.003 Å2-0 Å2-0 Å2
2---0.024 Å20 Å2
3---0.027 Å2
Refinement stepCycle: LAST / Resolution: 1.792→19.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1562 0 8 89 1659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131621
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171558
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.6542218
X-RAY DIFFRACTIONr_angle_other_deg1.3051.5633572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2035204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.46319.16772
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41615235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2121515
X-RAY DIFFRACTIONr_chiral_restr0.0740.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021796
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02364
X-RAY DIFFRACTIONr_nbd_refined0.2050.2265
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.21291
X-RAY DIFFRACTIONr_nbtor_refined0.1620.2756
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2733
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.276
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0010.21
X-RAY DIFFRACTIONr_nbd_other0.1470.228
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1340.24
X-RAY DIFFRACTIONr_mcbond_it1.9232.319821
X-RAY DIFFRACTIONr_mcbond_other1.8652.314819
X-RAY DIFFRACTIONr_mcangle_it2.7963.461020
X-RAY DIFFRACTIONr_mcangle_other2.8063.4631021
X-RAY DIFFRACTIONr_scbond_it2.4822.529800
X-RAY DIFFRACTIONr_scbond_other2.482.53801
X-RAY DIFFRACTIONr_scangle_it3.9053.6911197
X-RAY DIFFRACTIONr_scangle_other3.9033.6921198
X-RAY DIFFRACTIONr_lrange_it4.90527.1281679
X-RAY DIFFRACTIONr_lrange_other4.85327.0241668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.792-1.820.271940.2691671X-RAY DIFFRACTION94.6888
1.82-1.8380.177120.247292X-RAY DIFFRACTION86.6097
1.838-1.8890.286900.2411712X-RAY DIFFRACTION99.2291
1.889-1.9430.2711030.2351652X-RAY DIFFRACTION99.4334
1.943-2.0030.214960.1961598X-RAY DIFFRACTION100
2.003-2.0690.196910.2031578X-RAY DIFFRACTION99.8803
2.069-2.1410.231770.1991554X-RAY DIFFRACTION99.8164
2.141-2.2220.227640.1841478X-RAY DIFFRACTION100
2.222-2.3120.208780.191421X-RAY DIFFRACTION99.8003
2.312-2.4150.215800.1751358X-RAY DIFFRACTION100
2.415-2.5320.181690.1841325X-RAY DIFFRACTION100
2.532-2.6690.214620.1831262X-RAY DIFFRACTION100
2.669-2.830.232630.2031192X-RAY DIFFRACTION100
2.83-3.0240.226540.1861123X-RAY DIFFRACTION100
3.024-3.2660.188490.21066X-RAY DIFFRACTION99.9104
3.266-3.5750.176580.196972X-RAY DIFFRACTION99.6132
3.575-3.9940.179360.181879X-RAY DIFFRACTION99.2408
3.994-4.6060.185330.167795X-RAY DIFFRACTION98.1043
4.606-5.6260.252280.187668X-RAY DIFFRACTION97.3427
5.626-7.8930.313240.245538X-RAY DIFFRACTION98.4238

+
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