[English] 日本語
Yorodumi
- PDB-7k32: Crystal structure of Endonuclease Q complex with 27-mer duplex su... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7k32
TitleCrystal structure of Endonuclease Q complex with 27-mer duplex substrate with an abasic lesion at the active site
Components
  • (DNA (27-MER)) x 2
  • Endonuclease Q
KeywordsHYDROLASE/DNA / HYDROLASE / deamination / HYDROLASE-DNA complex
Function / homology
Function and homology information


Conserved hypothetical protein CHP00375 / Polymerase/histidinol phosphatase-like / Rubredoxin, iron-binding site / Rubredoxin signature. / Metal-dependent hydrolases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Phosphotransferase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsShi, K. / Moeller, N.M. / Banerjee, S. / Yin, L. / Orellana, K. / Aihara, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Structural basis for recognition of distinct deaminated DNA lesions by endonuclease Q.
Authors: Shi, K. / Moeller, N.H. / Banerjee, S. / McCann, J.L. / Carpenter, M.A. / Yin, L. / Moorthy, R. / Orellana, K. / Harki, D.A. / Harris, R.S. / Aihara, H.
History
DepositionSep 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endonuclease Q
B: DNA (27-MER)
C: DNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6936
Polymers61,5383
Non-polymers1553
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-67 kcal/mol
Surface area24010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.020, 154.020, 118.510
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

-
Components

#1: Protein Endonuclease Q


Mass: 44985.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: I6V2I0
#2: DNA chain DNA (27-MER)


Mass: 8356.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (27-MER)


Mass: 8196.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MG / MAGNESIUM ION


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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.44 Å3/Da / Density % sol: 72.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 15 mM Tris-HCl pH 7.4, 0.15 M NaCl, 1 mM MgCl2, and 4 mM beta-mercaptoethanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.11→88.6 Å / Num. obs: 17827 / % possible obs: 94.7 % / Redundancy: 2.2 % / Biso Wilson estimate: 121.63 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.097 / Rrim(I) all: 0.148 / Net I/σ(I): 7.4 / Num. measured all: 39581 / Scaling rejects: 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.11-3.332.31.002736832610.7480.8491.3181.296
8.8-88.62.20.03617337770.9910.030.0472493.3

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZB8

5zb8


Resolution: 3.11→88.59 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.17 / Phase error: 38.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2471 562 4.56 %
Rwork0.1994 11766 -
obs0.2016 12328 65.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 285.82 Å2 / Biso mean: 131.9871 Å2 / Biso min: 42.17 Å2
Refinement stepCycle: final / Resolution: 3.11→88.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3126 1093 3 0 4222
Biso mean--145.57 --
Num. residues----449
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.11-3.420.5707280.44455658412
3.42-3.920.43871130.34482709282260
3.92-4.930.26962070.24534222442994
4.93-88.590.20532140.14724279449395
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)
13.5984-0.65342.14078.52842.98457.77210.0957-0.2155-0.84060.94850.30130.03271.897-0.5559-0.38110.902-0.12760.19960.85110.00490.48621.731725.3318-18.7858
24.10570.47292.39475.3528-2.11213.64830.13490.43280.1624-0.3960.04960.55720.7943-0.9588-0.14530.61160.02560.00820.8962-0.04420.483620.507733.0727-30.3909
39.016-0.51233.43674.17310.48844.85190.23690.24610.4391-0.8263-0.2694-0.4896-0.01840.6390.19240.7128-0.01910.06380.87310.18780.538236.085737.9767-31.3679
48.63415.5665-3.97514.082-4.51777.8457-0.0307-0.0218-0.6352-0.3817-0.7167-0.70420.33140.82470.73910.53940.1632-0.0090.87220.14890.572937.375934.7406-20.3924
55.4398-2.3804-1.77394.66391.33879.8202-0.599-0.7399-0.5692-0.13830.3274-0.49550.86231.44550.2530.64070.03380.09010.59020.18710.698841.071232.487-23.1731
63.3268-0.25590.28233.9671-1.87598.272-0.00990.1409-0.37570.6726-0.2518-0.61481.17911.3750.28860.94780.4092-0.09220.8348-0.04150.786344.592227.0045-6.8226
70.9068-0.594-0.07853.9041-0.94892.7887-1.55821.0471-0.6022-2.00020.23280.70621.5690.19860.95023.0051-0.0656-0.10151.47130.03132.182135.6917-9.2678-0.9575
82.3304-0.64742.07232.9416-0.86438.88340.24730.8958-1.3375-0.48180.12180.78621.51821.0816-0.552.39420.3846-0.19411.1087-0.21691.548136.26486.4043-22.3902
93.7662-3.4045-3.76536.2195.32314.5522-0.70751.0737-0.31810.269-0.83150.61781.85071.58691.21812.09350.52830.4072.2672-0.18791.93841.776516.2406-52.8087
107.4118-1.4154-1.25067.59142.81912.14450.65240.8558-0.1265-0.5092-0.74760.704-0.3169-0.29660.53732.64431.81120.84732.5535-0.3822.522743.428517.747-72.282
116.8219-5.8175-3.89246.92546.75547.5830.99090.57131.06160.3869-0.93261.22871.91280.76580.06091.99210.54060.432.2282-0.37871.848842.577715.751-56.3678
121.9762-3.44293.12516.4422-4.24453.29581.07630.0785-1.3308-1.7118-0.39950.7153.28080.7359-0.67192.04730.0594-0.12491.0294-0.06551.40437.02635.3287-16.1393
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 54 )A1 - 54
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 131 )A55 - 131
3X-RAY DIFFRACTION3chain 'A' and (resid 132 through 173 )A132 - 173
4X-RAY DIFFRACTION4chain 'A' and (resid 174 through 205 )A174 - 205
5X-RAY DIFFRACTION5chain 'A' and (resid 206 through 278 )A206 - 278
6X-RAY DIFFRACTION6chain 'A' and (resid 279 through 395 )A279 - 395
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 5 )B1 - 5
8X-RAY DIFFRACTION8chain 'B' and (resid 6 through 15 )B6 - 15
9X-RAY DIFFRACTION9chain 'B' and (resid 17 through 26 )B17 - 26
10X-RAY DIFFRACTION10chain 'B' and (resid 27 through 27 )B27
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 10 )C1 - 10
12X-RAY DIFFRACTION12chain 'C' and (resid 11 through 27 )C11 - 27

+
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