[English] 日本語
Yorodumi
- PDB-3gpl: Crystal structure of the ternary complex of RecD2 with DNA and ADPNP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gpl
TitleCrystal structure of the ternary complex of RecD2 with DNA and ADPNP
Components
  • 5'-D(*T*TP*TP*TP*TP*TP*TP*T)-3'
  • Exodeoxyribonuclease V, subunit RecD, putative
KeywordsHYDROLASE/DNA / ALPHA AND BETA PROTEIN / ATP-BINDING / NUCLEOTIDE-BINDING / HELICASE / HYDROLASE-DNA COMPLEX
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 / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity ...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 / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / 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 / : / ATP-dependent RecD2 DNA helicase HHH domain / ATP-dependent RecD-like DNA helicase SH3 domain / ATP-dependent DNA helicase YrrC, OB-fold domain / UvrD-like helicase C-terminal 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 / : / ATP-dependent RecD2 DNA helicase HHH domain / ATP-dependent RecD-like DNA helicase SH3 domain / ATP-dependent DNA helicase YrrC, OB-fold 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 / Roll / P-loop containing nucleotide triphosphate hydrolases / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA / ATP-dependent RecD2 DNA helicase
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSaikrishnan, K. / Cook, N. / Wigley, D.B.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2009
Title: Mechanistic basis of 5'-3' translocation in SF1B helicases.
Authors: Saikrishnan, K. / Powell, B. / Cook, N.J. / Webb, M.R. / Wigley, D.B.
#1: Journal: 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
DepositionMar 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_ref_seq_dif / struct_site
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.ptnr1_label_seq_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.ptnr3_label_seq_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Exodeoxyribonuclease V, subunit RecD, putative
B: Exodeoxyribonuclease V, subunit RecD, putative
X: 5'-D(*T*TP*TP*TP*TP*TP*TP*T)-3'
Y: 5'-D(*T*TP*TP*TP*TP*TP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,7708
Polymers127,7094
Non-polymers1,0614
Water3,351186
1
A: Exodeoxyribonuclease V, subunit RecD, putative
X: 5'-D(*T*TP*TP*TP*TP*TP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3854
Polymers63,8542
Non-polymers5312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-19 kcal/mol
Surface area22790 Å2
MethodPISA
2
B: Exodeoxyribonuclease V, subunit RecD, putative
Y: 5'-D(*T*TP*TP*TP*TP*TP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3854
Polymers63,8542
Non-polymers5312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-19.3 kcal/mol
Surface area22760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.120, 130.360, 80.050
Angle α, β, γ (deg.)90.00, 107.34, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Exodeoxyribonuclease V, subunit RecD, putative


Mass: 61465.914 Da / Num. of mol.: 2 / Fragment: UNP residues 151-715
Source method: isolated from a genetically manipulated source
Details: N-terminus deletion mutant of RecD2
Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant)
Strain: R1 / DSM 20539 / IFO 15346 / LMG 4051 / NCIB 9279 / Gene: DR_1902, recD2 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9RT63
#2: DNA chain 5'-D(*T*TP*TP*TP*TP*TP*TP*T)-3'


Mass: 2388.585 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic DNA
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10% PEG 8000, 100 mM Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2Tris-HCl11
3PEG 800012
4Tris-HCl12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 20, 2008 / Details: mirrors
RadiationMonochromator: Varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 44807 / Num. obs: 44090 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 16.05
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 2 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 3.83 / Num. unique all: 4633 / Rsym value: 0.251 / % possible all: 94.6

-
Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
CNS1.2refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3E1S

3e1s


Resolution: 2.5→43.27 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1445846.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 2234 5.1 %RANDOM
Rwork0.232 ---
obs0.232 44090 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.1733 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 45.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å23 Å2
2---8.04 Å20 Å2
3---8.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.5→43.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7798 274 64 186 8322
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.353 364 5.1 %
Rwork0.325 6814 -
obs--96.5 %

+
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