[English] 日本語
Yorodumi
- PDB-5kn9: MutY N-terminal domain in complex with DNA containing an intrahel... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5kn9
TitleMutY N-terminal domain in complex with DNA containing an intrahelical oxoG:A base-pair
Components
  • Adenine DNA glycosylase
  • DNA (5'-D(*AP*GP*CP*AP*CP*AP*GP*GP*AP*T)-3')
  • DNA (5'-D(*AP*TP*CP*CP*(8OG)P*GP*TP*GP*CP*T)-3')
KeywordsHydrolase/DNA / adenine glycosylase / oxoG / DNA repair protein / intrahelical lesion recognition / Hydrolase-DNA complex
Function / homology
Function and homology information


adenine glycosylase / purine-specific mismatch base pair DNA N-glycosylase activity / DNA N-glycosylase activity / base-excision repair / 4 iron, 4 sulfur cluster binding / DNA binding / metal ion binding
Similarity search - Function
A/G-specific adenine glycosylase MutY / Iron-sulfur binding domain of endonuclease III / Adenine/Thymine-DNA glycosylase / MutY, C-terminal / NUDIX domain / Helix-hairpin-helix motif / Endonuclease III-like, iron-sulphur cluster loop motif / FES / Helix-hairpin-helix motif / Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) ...A/G-specific adenine glycosylase MutY / Iron-sulfur binding domain of endonuclease III / Adenine/Thymine-DNA glycosylase / MutY, C-terminal / NUDIX domain / Helix-hairpin-helix motif / Endonuclease III-like, iron-sulphur cluster loop motif / FES / Helix-hairpin-helix motif / Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) / Endonuclease Iii, domain 2 / Hypothetical protein; domain 2 / HhH-GPD superfamily base excision DNA repair protein / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / DNA glycosylase / Endonuclease III; domain 1 / NUDIX hydrolase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / DNA / Adenine DNA glycosylase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsWang, L. / Chakravarthy, S. / Verdine, G.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA100742 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural Basis for the Lesion-scanning Mechanism of the MutY DNA Glycosylase.
Authors: Wang, L. / Chakravarthy, S. / Verdine, G.L.
History
DepositionJun 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Apr 5, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adenine DNA glycosylase
C: DNA (5'-D(*AP*TP*CP*CP*(8OG)P*GP*TP*GP*CP*T)-3')
D: DNA (5'-D(*AP*GP*CP*AP*CP*AP*GP*GP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2566
Polymers32,8253
Non-polymers4323
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-44 kcal/mol
Surface area13200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.878, 38.759, 82.960
Angle α, β, γ (deg.)90.00, 105.66, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Adenine DNA glycosylase / oxoG:A-specific adenine glycosylase


Mass: 26694.490 Da / Num. of mol.: 1 / Fragment: UNP residues 1-229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus / Gene: mutY / Production host: Escherichia coli (E. coli)
References: UniProt: P83847, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds

-
DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(*AP*TP*CP*CP*(8OG)P*GP*TP*GP*CP*T)-3')


Mass: 3051.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Geobacillus stearothermophilus (bacteria)
#3: DNA chain DNA (5'-D(*AP*GP*CP*AP*CP*AP*GP*GP*AP*T)-3')


Mass: 3078.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Geobacillus stearothermophilus (bacteria)

-
Non-polymers , 3 types, 168 molecules

#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 300 mM Ca(OAc)2, 14% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.93→79.88 Å / Num. obs: 23193 / % possible obs: 99.5 % / Redundancy: 3.6 % / Net I/σ(I): 10.9
Reflection shellResolution: 1.93→1.98 Å / Rmerge(I) obs: 0.11

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RRQ

1rrq


Resolution: 1.93→79.879 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7
RfactorNum. reflection% reflection
Rfree0.2287 1187 5.12 %
Rwork0.1687 --
obs0.1718 23171 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.93→79.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1795 407 10 165 2377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082327
X-RAY DIFFRACTIONf_angle_d1.3163251
X-RAY DIFFRACTIONf_dihedral_angle_d19.335897
X-RAY DIFFRACTIONf_chiral_restr0.043348
X-RAY DIFFRACTIONf_plane_restr0.005353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9302-2.0180.30531410.22982724X-RAY DIFFRACTION100
2.018-2.12440.26661360.20752733X-RAY DIFFRACTION100
2.1244-2.25750.24471550.17712751X-RAY DIFFRACTION100
2.2575-2.43180.25781490.18032747X-RAY DIFFRACTION100
2.4318-2.67660.26761280.17492748X-RAY DIFFRACTION100
2.6766-3.06390.27051560.18232753X-RAY DIFFRACTION99
3.0639-3.86020.22531430.1472778X-RAY DIFFRACTION99
3.8602-79.94710.17881790.1512750X-RAY DIFFRACTION97
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)
16.95473.4591-2.60863.2406-4.79149.55430.16970.09570.39720.32570.110.8998-0.416-0.7928-0.24410.15960.03090.01470.2186-0.01430.287-15.38428.0023-11.0229
21.1761-0.2226-0.09182.5213-0.32916.308-0.22170.18540.181-0.68470.2116-0.1834-0.52060.2610.01690.3672-0.1331-0.020.23420.01970.1964-0.90837.039-31.378
31.4647-0.8041.10411.5432-1.70052.6819-0.08220.45990.1165-0.9675-0.0228-0.39440.15480.48580.25860.8046-0.3380.1730.58490.00780.16934.47230.3772-42.2879
47.6997-0.17556.70013.04462.0529.23370.1020.5179-0.1637-0.64050.0216-0.24410.21340.3445-0.21890.5729-0.15780.03790.3464-0.01380.16710.0147-7.1176-39.7554
55.306-1.98591.43720.8587-0.36876.1375-0.19670.3232-0.7019-0.2734-0.01090.30870.3068-0.28950.1580.4991-0.1771-0.05910.2687-0.02350.3026-10.4743-9.862-35.1166
60.81190.40221.32471.95111.42734.5096-0.0651-0.04770.0208-0.29330.05660.19220.0295-0.42520.00120.178-0.0799-0.05390.1740.03840.1805-8.1227-2.9198-19.67
74.3657-2.46410.4294.18140.48971.05470.0643-0.0036-0.38230.01530.00870.45120.4152-0.3129-0.07770.2285-0.1027-0.00820.21050.02820.1621-7.7763-9.9924-12.3505
86.15223.73782.99974.44192.41973.9162-0.13230.09350.4752-0.10330.07710.5493-0.1048-0.22460.05270.1855-0.0631-0.04310.16420.05360.2206-11.35183.9972-18.1496
94.1337-0.5724-2.09087.11761.216.5525-0.1525-0.08160.6273-0.14070.0878-0.4756-0.56110.42330.07260.2298-0.074-0.04690.12820.02620.1783-0.48448.0714-6.6452
105.7579-4.5419-1.1848.06031.38334.624-0.3183-0.3501-0.10170.74940.2535-0.16120.41540.10910.03130.2382-0.0446-0.03170.11590.02180.1362-1.8299-1.0667-2.3419
114.70993.50930.34184.079-1.40183.1553-0.19720.1328-0.1663-0.4370.0548-0.7760.22730.65230.05370.2171-0.03840.07220.323-0.07550.431511.8715-9.5652-21.9416
125.0819-0.71020.09620.1855-0.26031.09470.1415-0.5411-0.2855-0.4974-0.0682-0.99480.00320.157-0.10280.259-0.10040.01640.31770.02590.509110.1363-9.578-20.5985
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 88 )
4X-RAY DIFFRACTION4chain 'A' and (resid 89 through 105 )
5X-RAY DIFFRACTION5chain 'A' and (resid 106 through 124 )
6X-RAY DIFFRACTION6chain 'A' and (resid 125 through 155 )
7X-RAY DIFFRACTION7chain 'A' and (resid 156 through 179 )
8X-RAY DIFFRACTION8chain 'A' and (resid 180 through 196 )
9X-RAY DIFFRACTION9chain 'A' and (resid 197 through 210 )
10X-RAY DIFFRACTION10chain 'A' and (resid 211 through 229 )
11X-RAY DIFFRACTION11chain 'C' and (resid 3 through 12 )
12X-RAY DIFFRACTION12chain 'D' and (resid 13 through 22 )

+
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