[English] 日本語
Yorodumi
- PDB-4mgt: ALKBH2 R110A cross-linked to undamaged dsDNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mgt
TitleALKBH2 R110A cross-linked to undamaged dsDNA
Components
  • Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2
  • DNA1
  • DNA2
KeywordsOXIDOREDUCTASE/DNA / protein-DNA complex / OXIDOREDUCTASE-DNA complex
Function / homology
Function and homology information


cytosine C-5 DNA demethylase activity / ALKBH2 mediated reversal of alkylation damage / DNA oxidative demethylase / broad specificity oxidative DNA demethylase activity / rDNA binding / DNA alkylation repair / ferrous iron binding / nucleolus / nucleoplasm / nucleus
Similarity search - Function
DNA oxidative demethylase ALKBH2 / Alpha-ketoglutarate-dependent dioxygenase AlkB-like / 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. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA oxidative demethylase ALKBH2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsChen, B. / Gan, J. / Yang, C.G.
CitationJournal: Sci China Chem / Year: 2014
Title: The complex structures of ALKBH2 mutants cross-linked to dsDNA reveal the conformational swing of β-hairpin
Authors: Chen, B. / Gan, J. / Yang, C.G.
History
DepositionAug 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Non-polymer description
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2
B: DNA1
C: DNA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5704
Polymers31,5463
Non-polymers241
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-25 kcal/mol
Surface area14140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.099, 129.099, 84.466
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

-
Components

#1: Protein Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2 / Alkylated DNA repair protein alkB homolog 2 / DNA oxidative demethylase ALKBH2 / Oxy DC1


Mass: 23238.545 Da / Num. of mol.: 1 / Fragment: UNP residues 56-258 / Mutation: R110A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALKBH2, ABH2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NS38, DNA oxidative demethylase
#2: DNA chain DNA1


Mass: 4313.831 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesis
#3: DNA chain DNA2


Mass: 3993.676 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesis
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% PEG 5000, 100mM sodium chloride, 50mM Magnesium chloride, 100mM cacodylate, pH 6.5, vapor diffusion, hanging drop, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2010
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionRedundancy: 27.6 % / Number: 369194 / Rmerge(I) obs: 0.101 / Χ2: 1.06 / D res high: 2.6 Å / D res low: 50 Å / Num. obs: 13363 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.65099.710.0471.09129.7
4.455.610010.071.00132
3.884.4599.910.0831.09133
3.533.8810010.1241.04633.3
3.283.5399.910.1951.13133.4
3.083.2899.810.2961.132.4
2.933.0899.910.431.00629.5
2.82.9399.710.6041.00524.4
2.692.899.310.830.99417
2.62.6995.110.8941.0469.7
ReflectionResolution: 2.6→50 Å / Num. all: 13880 / Num. obs: 13760 / % possible obs: 99.2 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.8
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.6-2.69195.1
2.69-2.8199.3
2.8-2.93199.7
2.93-3.08199.9
3.08-3.28199.8
3.28-3.53199.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3S5A

3s5a


Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.906 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 21.869 / SU ML: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.448 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2759 649 4.9 %RANDOM
Rwork0.2306 ---
obs0.233 13200 99.38 %-
all-13849 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.4 Å2 / Biso mean: 70.637 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20.41 Å2-0 Å2
2--0.41 Å2-0 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1600 550 1 0 2151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0172271
X-RAY DIFFRACTIONr_bond_other_d0.0010.021886
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.713180
X-RAY DIFFRACTIONr_angle_other_deg0.95434345
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.595200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.56621.92378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.16915274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5351516
X-RAY DIFFRACTIONr_chiral_restr0.0820.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022167
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02550
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.487 44 -
Rwork0.398 858 -
all-902 -
obs--95.05 %
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)
12.29610.3991-0.44122.02760.06110.82630.0754-0.05270.19470.0060.1311-0.0687-0.08540.0888-0.20650.0893-0.04610.09240.1134-0.01570.143638.5321-35.7958-3.9841
24.0321-2.07942.96214.0644-3.635310.5692-0.051-0.23120.20870.27720.2095-0.2432-0.4956-0.1955-0.15850.1365-0.10770.08640.149-0.11560.115548.5332-18.5386.019
35.2287-0.53770.80774.0922-2.4966.31680.04610.0436-0.07450.22010.09130.04-0.90460.3679-0.13740.3126-0.19640.10690.2411-0.19340.185350.5074-18.05126.0938
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A55 - 259
2X-RAY DIFFRACTION2B10 - 23
3X-RAY DIFFRACTION3C28 - 40

+
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