[English] 日本語
Yorodumi
- PDB-5gke: Structure of EndoMS-dsDNA1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gke
TitleStructure of EndoMS-dsDNA1 complex
Components
  • DNA (5'-D(*CP*GP*CP*TP*AP*CP*AP*TP*GP*TP*CP*GP*TP*CP*C)-3')
  • DNA (5'-D(*GP*GP*AP*CP*GP*AP*CP*GP*TP*GP*TP*AP*GP*CP*G)-3')
  • Endonuclease EndoMS
KeywordsHYDROLASE/DNA / ENDONUCLEASES / DNA-BINDING / HYDROLASE-DNA complex
Function / homology
Function and homology information


single-stranded DNA endodeoxyribonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / cytoplasm
Similarity search - Function
Protein Yojf; Chain: A; - #20 / Protein Yojf; Chain: A; / Endonuclease NucS / : / : / : / Endonuclease NucS C-terminal domain / Endonuclease NucS N-terminal PH-like domain / Trna Endonuclease; Chain: A, domain 1 - #10 / Trna Endonuclease; Chain: A, domain 1 ...Protein Yojf; Chain: A; - #20 / Protein Yojf; Chain: A; / Endonuclease NucS / : / : / : / Endonuclease NucS C-terminal domain / Endonuclease NucS N-terminal PH-like domain / Trna Endonuclease; Chain: A, domain 1 - #10 / Trna Endonuclease; Chain: A, domain 1 / tRNA endonuclease-like domain superfamily / Distorted Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Endonuclease NucS
Similarity search - Component
Biological speciesThermococcus kodakarensis KOD1 (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNakae, S. / Hijikata, A. / Tsuji, T. / Yonezawa, K. / Kouyama, K. / Mayanagi, K. / Ishino, S. / Ishino, Y. / Shirai, T.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Agency for Medical Research and DevelopmentDrug Discovery and Life Science Research(Platform for Drug Discovery, Informatics and Structural Life Science) Japan
Ministry of Education, Culture, Sports, Science and Technology25280109 Japan
Ministry of Education, Culture, Sports, Science and Technology26242075 Japan
CitationJournal: Structure / Year: 2016
Title: Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease
Authors: Nakae, S. / Hijikata, A. / Tsuji, T. / Yonezawa, K. / Kouyama, K.I. / Mayanagi, K. / Ishino, S. / Ishino, Y. / Shirai, T.
History
DepositionJul 4, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endonuclease EndoMS
B: Endonuclease EndoMS
C: DNA (5'-D(*CP*GP*CP*TP*AP*CP*AP*TP*GP*TP*CP*GP*TP*CP*C)-3')
D: DNA (5'-D(*GP*GP*AP*CP*GP*AP*CP*GP*TP*GP*TP*AP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,03211
Polymers66,3924
Non-polymers6397
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14130 Å2
ΔGint-138 kcal/mol
Surface area22710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.360, 92.360, 404.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Endonuclease EndoMS / Endonuclease NucS


Mass: 28598.096 Da / Num. of mol.: 2 / Mutation: D165A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis KOD1 (archaea)
Strain: KOD1 / Gene: TK1898 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5JER9, Hydrolases; Acting on ester bonds

-
DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(*CP*GP*CP*TP*AP*CP*AP*TP*GP*TP*CP*GP*TP*CP*C)-3')


Mass: 4520.935 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*GP*AP*CP*GP*AP*CP*GP*TP*GP*TP*AP*GP*CP*G)-3')


Mass: 4675.034 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 3 types, 73 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 3.93 Å3/Da / Density % sol: 68.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: CALCIUM ACETATE, SODIUM CACODYLATE, PEG8000, GLYCEROL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→24.79 Å / Num. obs: 40879 / % possible obs: 98.8 % / Redundancy: 3.9 % / Rsym value: 0.012 / Net I/σ(I): 96.2
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 9.1 / % possible all: 94.6

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
MOSFLMdata scaling
PHASERphasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VLD, 1DC1

2vld

1dc1


Resolution: 2.4→24.79 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.43
RfactorNum. reflection% reflection
Rfree0.244 2009 5.02 %
Rwork0.19 --
obs0.192 40005 97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→24.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3800 610 42 66 4518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085259
X-RAY DIFFRACTIONf_angle_d1.2337350
X-RAY DIFFRACTIONf_dihedral_angle_d21.8092122
X-RAY DIFFRACTIONf_chiral_restr0.047835
X-RAY DIFFRACTIONf_plane_restr0.007734
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.46010.3661230.362443X-RAY DIFFRACTION89
2.4601-2.52650.42031330.31922476X-RAY DIFFRACTION91
2.5265-2.60080.39341510.3042497X-RAY DIFFRACTION92
2.6008-2.68460.32961160.28962641X-RAY DIFFRACTION96
2.6846-2.78040.31061430.26582647X-RAY DIFFRACTION97
2.7804-2.89160.36591470.24342703X-RAY DIFFRACTION98
2.8916-3.0230.26071610.22482668X-RAY DIFFRACTION98
3.023-3.18210.24551340.19642750X-RAY DIFFRACTION99
3.1821-3.3810.24891510.17942738X-RAY DIFFRACTION99
3.381-3.64130.22891450.16112788X-RAY DIFFRACTION99
3.6413-4.00630.20171190.16022857X-RAY DIFFRACTION100
4.0063-4.58290.17411610.13382812X-RAY DIFFRACTION100
4.5829-5.7620.19181630.14792892X-RAY DIFFRACTION100
5.762-24.79310.2351620.18113084X-RAY DIFFRACTION100

+
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