[English] 日本語
Yorodumi
- PDB-5dac: ATP-gamma-S bound Rad50 from Chaetomium thermophilum in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dac
TitleATP-gamma-S bound Rad50 from Chaetomium thermophilum in complex with DNA
Components
  • DNA (5'-D(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3')
  • DNA (5'-D(P*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3')
  • Putative uncharacterized protein,Putative uncharacterized protein
KeywordsHYDROLASE / ATPase / ATPyS bound
Function / homology
Function and homology information


Mre11 complex / chromosome organization involved in meiotic cell cycle / Hydrolases; Acting on acid anhydrides / G-quadruplex DNA binding / double-stranded telomeric DNA binding / telomere maintenance via recombination / single-stranded telomeric DNA binding / DNA duplex unwinding / telomere maintenance via telomerase / guanyl-nucleotide exchange factor activity ...Mre11 complex / chromosome organization involved in meiotic cell cycle / Hydrolases; Acting on acid anhydrides / G-quadruplex DNA binding / double-stranded telomeric DNA binding / telomere maintenance via recombination / single-stranded telomeric DNA binding / DNA duplex unwinding / telomere maintenance via telomerase / guanyl-nucleotide exchange factor activity / condensed nuclear chromosome / double-strand break repair / double-stranded DNA binding / ATP hydrolysis activity / metal ion binding
Similarity search - Function
DNA repair protein Rad50, eukaryotes / SbcC/RAD50-like, Walker B motif / Rad50/SbcC-type AAA domain / AAA domain / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / DNA repair protein RAD50
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.503 Å
AuthorsSeifert, F.U. / Lammens, K. / Stoehr, G. / Kessler, B. / Hopfner, K.-P.
CitationJournal: Embo J. / Year: 2016
Title: Structural mechanism of ATP-dependent DNA binding and DNA end bridging by eukaryotic Rad50.
Authors: Seifert, F.U. / Lammens, K. / Stoehr, G. / Kessler, B. / Hopfner, K.P.
History
DepositionAug 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Apr 13, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: 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
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.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.value / _struct_conn.pdbx_dist_value / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein,Putative uncharacterized protein
B: Putative uncharacterized protein,Putative uncharacterized protein
C: DNA (5'-D(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3')
D: DNA (5'-D(P*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,40210
Polymers109,9014
Non-polymers1,5026
Water1,874104
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9070 Å2
ΔGint-46 kcal/mol
Surface area45400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.312, 97.078, 115.012
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Putative uncharacterized protein,Putative uncharacterized protein


Mass: 50357.375 Da / Num. of mol.: 2 / Mutation: E1238Q,E1238Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0073630 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SHW7

-
DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3')


Mass: 4292.769 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3')


Mass: 4893.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 110 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-AES / 4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / AEBSF


Mass: 203.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10FNO2S / Comment: protease inhibitor*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.25 M potassium acetate, 42% (v/v) pentaerythritol propoxylate (5/4 PO/OH)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9716 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9716 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 36106 / % possible obs: 99.5 % / Redundancy: 12.8 % / Rsym value: 0.2 / Net I/σ(I): 11.96
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 12.6 % / Rmerge(I) obs: 1.85 / Mean I/σ(I) obs: 1.33 / % possible all: 97

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5da9

5da9


Resolution: 2.503→49.477 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2458 1805 5 %
Rwork0.2103 --
obs0.2121 36099 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.503→49.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6831 615 90 104 7640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087699
X-RAY DIFFRACTIONf_angle_d1.19210510
X-RAY DIFFRACTIONf_dihedral_angle_d18.2942989
X-RAY DIFFRACTIONf_chiral_restr0.051207
X-RAY DIFFRACTIONf_plane_restr0.0051235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.503-2.57070.36331280.32752423X-RAY DIFFRACTION94
2.5707-2.64630.33361370.29962610X-RAY DIFFRACTION100
2.6463-2.73170.29961380.27472613X-RAY DIFFRACTION100
2.7317-2.82940.28251370.262605X-RAY DIFFRACTION100
2.8294-2.94260.27551400.26642659X-RAY DIFFRACTION100
2.9426-3.07650.30341370.25832602X-RAY DIFFRACTION100
3.0765-3.23870.29931380.27222620X-RAY DIFFRACTION100
3.2387-3.44160.32051390.24722640X-RAY DIFFRACTION100
3.4416-3.70720.28171400.21752663X-RAY DIFFRACTION100
3.7072-4.08010.23671390.20332651X-RAY DIFFRACTION100
4.0801-4.67020.21071410.16192671X-RAY DIFFRACTION100
4.6702-5.88240.20661420.17972708X-RAY DIFFRACTION100
5.8824-49.48640.18741490.1742829X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 39.4474 Å / Origin y: 38.8463 Å / Origin z: 49.1344 Å
111213212223313233
T0.1631 Å20.0075 Å20.0472 Å2-0.4339 Å20.0403 Å2--0.4212 Å2
L0.4808 °20.1647 °20.3134 °2-0.5783 °20.0383 °2--0.3465 °2
S-0.0517 Å °-0.0446 Å °-0.1483 Å °-0.0231 Å °0.0048 Å °-0.1794 Å °0.0526 Å °0.0427 Å °0.0403 Å °
Refinement TLS groupSelection details: all

+
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://pdbjlvh1.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