[English] 日本語
Yorodumi
- PDB-2fd8: Crystal Structure of AlkB in complex with Fe(II), 2-oxoglutarate,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fd8
TitleCrystal Structure of AlkB in complex with Fe(II), 2-oxoglutarate, and methylated trinucleotide T-meA-T
Components
  • 5'-D(P*TP*(MA7)P*T)-3'
  • Alkylated DNA repair protein alkB
KeywordsOXIDOREDUCTASE/DNA / beta jellyroll / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / OXIDOREDUCTASE-DNA COMPLEX
Function / homology
Function and homology information


response to methyl methanesulfonate / oxidative RNA demethylation / DNA oxidative demethylase / : / : / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / RNA repair / DNA alkylation repair ...response to methyl methanesulfonate / oxidative RNA demethylation / DNA oxidative demethylase / : / : / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / RNA repair / DNA alkylation repair / oxidative demethylation / DNA demethylation / dioxygenase activity / ferrous iron binding / DNA repair / cytoplasm
Similarity search - Function
Alkylated DNA repair protein AlkB / 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
2-OXOGLUTARIC ACID / : / DNA / Alpha-ketoglutarate-dependent dioxygenase AlkB
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsYu, B. / Benach, J. / Edstrom, W.C. / Gibney, B.R. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Nature / Year: 2006
Title: Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB.
Authors: Yu, B. / Edstrom, W.C. / Benach, J. / Hamuro, Y. / Weber, P.C. / Gibney, B.R. / Hunt, J.F.
History
DepositionDec 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 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 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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
Remark 600HETEROGEN The close contacts in remark 500 are due to iron coordination.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: 5'-D(P*TP*(MA7)P*T)-3'
A: Alkylated DNA repair protein alkB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7054
Polymers24,5032
Non-polymers2022
Water3,855214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.746, 40.746, 118.304
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

-
Components

#1: DNA chain 5'-D(P*TP*(MA7)P*T)-3'


Mass: 891.669 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein Alkylated DNA repair protein alkB


Mass: 23610.975 Da / Num. of mol.: 1 / Fragment: residues 12-216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: alkB, aidD / Plasmid: pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P05050
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / 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 Å3/Da / Density % sol: 38.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 22-24% (w/v) PEG 3350, 10% glycerol and 200 mM sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.74060, 1.74169, 1.70473
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 19, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.74061
21.741691
31.704731
Reflection

D res high: 2.3 Å / D res low: 20 Å

Redundancy (%)IDNumberRmerge(I) obsΧ2% possible obs
7.81169580.0571.39899.6
8.12170210.061.10999.6
8.13171010.0721.08699.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.932099.810.0431.4738.3
3.934.9310010.0451.6598.4
3.433.9310010.0521.7668.3
3.123.4310010.0591.6138.2
2.93.1210010.0661.4348.1
2.732.910010.0761.2698
2.592.7310010.0871.1567.9
2.482.5910010.1031.0987.9
2.382.4810010.1251.1816.9
2.32.3896.510.1321.1845.5
4.932099.920.0431.2468.8
3.934.9310020.0461.4438.8
3.433.9310020.0551.4818.7
3.123.4310020.0611.3028.6
2.93.1210020.0711.0868.5
2.732.910020.0860.9818.4
2.592.7310020.0990.8788.3
2.482.5910020.1190.8018.3
2.382.4810020.1430.8117.1
2.32.3895.820.1560.8525.5
4.932010030.0481.3178.8
3.934.9310030.0541.678.8
3.433.9310030.0661.6298.7
3.123.4310030.0741.3388.6
2.93.1210030.0881.0348.5
2.732.910030.1060.8558.4
2.592.7310030.1290.7238.3
2.482.5910030.1550.6328.1
2.382.4810030.1890.6357.3
2.32.3896.730.2040.6835.2
ReflectionResolution: 2.3→20 Å / Num. obs: 8630 / % possible obs: 99.8 % / Redundancy: 15.3 % / Rmerge(I) obs: 0.066 / Χ2: 1.066
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.3810.80.1438360.779197.7
2.38-2.4813.70.1358520.8041100
2.48-2.5915.60.1138720.7621100
2.59-2.7315.70.0988710.8281100
2.73-2.915.90.0868580.9371100
2.9-3.1216.10.0758611.0561100
3.12-3.4316.10.0668661.1651100
3.43-3.9316.40.068571.2861100
3.93-4.9316.50.0538601.3171100
4.93-2016.10.0558971.5311100

-
Phasing

PhasingMethod: MAD
Phasing MAD set siteAtom type symbol: Fe / B iso: 17.912 / Fract x: 0.424 / Fract y: 0.028 / Fract z: 0 / Occupancy: 1.273
Phasing dmFOM : 0.67 / FOM acentric: 0.67 / FOM centric: 0.62 / Reflection: 8538 / Reflection acentric: 8297 / Reflection centric: 241
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.6-29.5760.870.870.8237434529
4.1-6.60.780.780.721137109146
3.3-4.10.660.660.641451140546
2.9-3.30.710.710.661437140235
2.5-2.90.670.670.52577252156
2.3-2.50.540.540.441562153329

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.08phasing
RESOLVE2.08phasing
CNS1.1refinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1476777 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.227 894 10.5 %RANDOM
Rwork0.186 ---
obs-8536 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.089 Å2 / ksol: 0.313 e/Å3
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å20 Å20 Å2
2---0.92 Å20 Å2
3---2.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1556 63 11 214 1844
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_improper_angle_d1.42
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.282
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it2.92.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 138 9.9 %
Rwork0.201 1257 -
obs-1395 98.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3dna-rna_rep.param_bydna-rna.top_by
X-RAY DIFFRACTION4ion.paramion.top

+
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