[English] 日本語
Yorodumi
- PDB-3e1s: Structure of an N-terminal truncation of Deinococcus radiodurans RecD2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3e1s
TitleStructure of an N-terminal truncation of Deinococcus radiodurans RecD2
ComponentsExodeoxyribonuclease V, subunit RecD
KeywordsHYDROLASE / alpha and beta protein / ATP-binding / Nucleotide-binding
Function / homology
Function and homology information


exodeoxyribonuclease V complex / DNA 5'-3' helicase / single-stranded DNA helicase activity / ATP-dependent activity, acting on DNA / isomerase activity / 5'-3' DNA helicase activity / DNA recombination / ATP hydrolysis activity / DNA binding / ATP binding
Similarity search - Function
Arc Repressor Mutant, subunit A - #2220 / SH3 type barrels. - #940 / RecD-like DNA helicase / RecD helicase-like helix-hairpin-helix domain / RecD-like DNA helicase, SH3 domain / Helix-hairpin-helix containing domain / ATP-dependent RecD-like DNA helicase SH3 domain / UvrD-like helicase C-terminal domain / UvrD-like helicase C-terminal domain / AAA domain ...Arc Repressor Mutant, subunit A - #2220 / SH3 type barrels. - #940 / RecD-like DNA helicase / RecD helicase-like helix-hairpin-helix domain / RecD-like DNA helicase, SH3 domain / Helix-hairpin-helix containing domain / ATP-dependent RecD-like DNA helicase SH3 domain / UvrD-like helicase C-terminal domain / UvrD-like helicase C-terminal domain / AAA domain / Helix-hairpin-helix domain / SH3 type barrels. / Arc Repressor Mutant, subunit A / P-loop containing nucleotide triphosphate hydrolases / Roll / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ATP-dependent RecD2 DNA helicase
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å
AuthorsSaikrishnan, K. / Griffiths, S.P. / Cook, N. / Court, R. / Wigley, D.B.
CitationJournal: Embo J. / Year: 2008
Title: DNA binding to RecD: role of the 1B domain in SF1B helicase activity.
Authors: Saikrishnan, K. / Griffiths, S.P. / Cook, N. / Court, R. / Wigley, D.B.
History
DepositionAug 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Exodeoxyribonuclease V, subunit RecD


Theoretical massNumber of molelcules
Total (without water)61,4661
Polymers61,4661
Non-polymers00
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.630, 89.630, 131.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Exodeoxyribonuclease V, subunit RecD


Mass: 61465.914 Da / Num. of mol.: 1
Fragment: N-terminus deletion mutant of RecD2, UNP residues 151-715
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: recD / Plasmid: pET22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9RT63
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.62 Å3/Da / Density % sol: 53.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 13-18% ethanol, 100mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07225 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 3, 2007
RadiationMonochromator: Single Silicon (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07225 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 33616 / Num. obs: 32947 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 15.2
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 2.25 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 3.2 / Num. unique all: 4035 / % possible all: 98

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DNAdata collection
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→20.7 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.911 / SU B: 16.458 / SU ML: 0.219 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.29 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28744 2668 8.1 %RANDOM
Rwork0.2308 ---
all0.23541 32946 --
obs0.23541 30278 98.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.288 Å2
Baniso -1Baniso -2Baniso -3
1-3.38 Å20 Å20 Å2
2---4.09 Å20 Å2
3---0.71 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3889 0 0 265 4154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213962
X-RAY DIFFRACTIONr_bond_other_d0.0020.022671
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.9725382
X-RAY DIFFRACTIONr_angle_other_deg0.88936493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7595513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96322.934167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.94215636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7191537
X-RAY DIFFRACTIONr_chiral_restr0.070.2619
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024463
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02789
X-RAY DIFFRACTIONr_nbd_refined0.2010.2971
X-RAY DIFFRACTIONr_nbd_other0.20.22870
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21906
X-RAY DIFFRACTIONr_nbtor_other0.0880.22177
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.205
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.146
X-RAY DIFFRACTIONr_symmetry_vdw_other0.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.095
X-RAY DIFFRACTIONr_mcbond_it0.499
X-RAY DIFFRACTIONr_mcbond_other0.092
X-RAY DIFFRACTIONr_mcangle_it0.607
X-RAY DIFFRACTIONr_scbond_it1.004
X-RAY DIFFRACTIONr_scangle_it1.515
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 181 -
Rwork0.284 2161 -
obs--97.54 %
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)
15.22641.0467-1.64145.48653.785713.32980.0301-0.40770.75220.2057-0.25860.353-1.8931-1.3040.22850.30330.1817-0.1215-0.1632-0.025-0.0828-2.4868-7.529547.6344
21.94082.0984.28556.63044.800612.38980.189-0.1575-0.3672-0.0020.1279-0.37291.12690.1461-0.3169-0.0913-0.0071-0.0558-0.2290.0578-0.1636-0.6743-27.244934.5342
31.19560.48660.81865.0759-0.86984.35480.05370.0378-0.0794-0.79440.25220.33230.9875-0.5318-0.3059-0.0187-0.164-0.1371-0.19330.0557-0.1889-11.0239-23.860315.6866
43.7022-0.2033-0.15376.84740.27273.7087-0.11940.08780.1685-0.7578-0.1354-0.2767-0.03190.1920.2547-0.2771-0.0673-0.0015-0.23040.0564-0.2425-2.45422.53811.9518
57.45151.29761.201314.7457-1.5065.57370.2555-0.59940.21440.3567-0.22651.1295-0.169-0.7545-0.0291-0.35640.01370.02690.2383-0.0980.1674-25.77523.012122.3798
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA193 - 27444 - 125
2X-RAY DIFFRACTION2AA275 - 322126 - 173
3X-RAY DIFFRACTION2AA704 - 720555 - 571
4X-RAY DIFFRACTION3AA339 - 491190 - 342
5X-RAY DIFFRACTION4AA492 - 574343 - 425
6X-RAY DIFFRACTION4AA640 - 703491 - 554
7X-RAY DIFFRACTION5AA575 - 639426 - 490

+
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