[English] 日本語
Yorodumi
- PDB-2boo: The crystal structure of Uracil-DNA N-Glycosylase (UNG) from Dein... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2boo
TitleThe crystal structure of Uracil-DNA N-Glycosylase (UNG) from Deinococcus radiodurans.
ComponentsURACIL-DNA GLYCOSYLASE
KeywordsHYDROLASE / BASE EXCISION REPAIR / RADIATION RESISTANCE / DNA DAMAGE / DNA REPAIR / GLYCOSIDASE
Function / homology
Function and homology information


base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / uracil DNA N-glycosylase activity / cytoplasm
Similarity search - Function
Uracil-DNA glycosylase family 1 / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily ...Uracil-DNA glycosylase family 1 / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLeiros, I. / Moe, E. / Smalas, A.O. / McSweeney, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of the Uracil-DNA N-Glycosylase (Ung) from Deinococcus Radiodurans.
Authors: Leiros, I. / Moe, E. / Smalas, A.O. / Mcsweeney, S.
History
DepositionApr 13, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 3, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_data_processing_status / pdbx_database_proc / pdbx_database_status / pdbx_validate_close_contact / struct_biol / struct_conn / struct_conn_type
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: URACIL-DNA GLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9674
Polymers27,7811
Non-polymers1863
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.500, 85.100, 85.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein URACIL-DNA GLYCOSYLASE / UDG


Mass: 27780.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: RESIDUES 1-16 AND 247 NOT VISIBLE IN ELECTRON DENSITY
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Strain: R1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RWH9, uridine nucleosidase
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Compound detailsEXCISES URACIL RESIDUES FROM THE DNA

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.1 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 277 K / pH: 7.5
Details: 0.2 M AMMONIUM NITRATE, 17% (W/V) PEG 3000 AT 4 DEGREES C, pH 7.50

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 3, 2003 / Details: TOROIDAL MIRROR
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.8→28.36 Å / Num. obs: 40425 / % possible obs: 93.7 % / Observed criterion σ(I): 0 / Redundancy: 2.52 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 4.44
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.37 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.65 / % possible all: 95.2

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AKZ

1akz


Resolution: 1.8→84.52 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.903 / SU B: 9.074 / SU ML: 0.119 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SUB-OPTIMAL REFINEMENT STATISTICS CAUSED BY CRYSTALS CONSISTING OF SEVERAL LATTICES. FLEXIBLE REGIONS IN PROTEIN CAN NOT BE MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.272 2038 5 %RANDOM
Rwork0.234 ---
obs0.236 38387 92.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.19 Å2
Baniso -1Baniso -2Baniso -3
1--2.37 Å20 Å20 Å2
2---2.59 Å20 Å2
3---4.95 Å2
Refinement stepCycle: LAST / Resolution: 1.8→84.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1839 0 12 154 2005
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221910
X-RAY DIFFRACTIONr_bond_other_d0.0070.021713
X-RAY DIFFRACTIONr_angle_refined_deg1.8411.9612598
X-RAY DIFFRACTIONr_angle_other_deg1.00233999
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9135229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.57323.52388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.26415304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9761512
X-RAY DIFFRACTIONr_chiral_restr0.1110.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022114
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02389
X-RAY DIFFRACTIONr_nbd_refined0.2260.2401
X-RAY DIFFRACTIONr_nbd_other0.2070.21658
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2906
X-RAY DIFFRACTIONr_nbtor_other0.0890.2920
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.2117
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2620.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9651.51512
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.72721870
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.9663998
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2054.5728
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.324 166
Rwork0.31 2826
Refinement TLS params.Method: refined / Origin x: 19.2288 Å / Origin y: 11.1286 Å / Origin z: 43.9299 Å
111213212223313233
T-0.0039 Å20.0049 Å20.0057 Å2-0.0112 Å2-0.0072 Å2---0.0952 Å2
L0.784 °20.2295 °2-0.2922 °2-1.2951 °2-0.4196 °2--0.4657 °2
S-0.0637 Å °0.0311 Å °0.1198 Å °-0.0587 Å °0.0704 Å °0.0442 Å °0.0571 Å °-0.0388 Å °-0.0067 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 246
2X-RAY DIFFRACTION1A1247 - 1249

+
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