[English] 日本語
Yorodumi
- PDB-6s3h: Crystal structure of helicase Pif1 from Thermus oshimai in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6s3h
TitleCrystal structure of helicase Pif1 from Thermus oshimai in complex with ADP-AlF4 and (dT)7ds11bp
Components
  • DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
  • PIF1 helicase
KeywordsHYDROLASE / DNA helicase
Function / homology
Function and homology information


telomere maintenance / DNA helicase activity / DNA repair / nucleotide binding / metal ion binding
Similarity search - Function
: / DNA helicase Pif1-like / PIF1-like helicase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / DNA / PIF1 helicase
Similarity search - Component
Biological speciesThermus oshimai JL-2 (bacteria)
Thermus oshimai (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsDai, Y.X. / Chen, W.F. / Teng, F.Y. / Liu, N.N. / Hou, X.M. / Dou, S.X. / Rety, S. / Xi, X.G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370798,11304252,11574252,31301632 China
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structural and functional studies of SF1B Pif1 from Thermus oshimai reveal dimerization-induced helicase inhibition.
Authors: Dai, Y.X. / Chen, W.F. / Liu, N.N. / Teng, F.Y. / Guo, H.L. / Hou, X.M. / Dou, S.X. / Rety, S. / Xi, X.G.
History
DepositionJun 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 28, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: 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: PIF1 helicase
B: PIF1 helicase
D: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
E: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,15910
Polymers105,0504
Non-polymers1,1096
Water8,935496
1
A: PIF1 helicase
D: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0805
Polymers52,5252
Non-polymers5543
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-29 kcal/mol
Surface area19090 Å2
MethodPISA
2
B: PIF1 helicase
E: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0805
Polymers52,5252
Non-polymers5543
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-24 kcal/mol
Surface area19780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.682, 200.130, 53.955
Angle α, β, γ (deg.)90.00, 93.44, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein / DNA chain , 2 types, 4 molecules ABDE

#1: Protein PIF1 helicase


Mass: 50440.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus oshimai JL-2 (bacteria) / Gene: Theos_1468 / Plasmid: plasmid / Details (production host): pET15b-SUMO / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): C2566H / References: UniProt: K7RJ88
#2: DNA chain DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')


Mass: 2084.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermus oshimai (bacteria)

-
Non-polymers , 4 types, 502 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Sodium Hepes-MOPS 0.1M CaCl2 0.03M MgCl2 0.03M PEG 8000 10% Ethylene glycol 20%

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9779 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 2.057→53.86 Å / Num. obs: 66828 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 36.91 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.0682 / Rpim(I) all: 0.0338 / Rrim(I) all: 0.08108 / Net I/σ(I): 10.71
Reflection shellResolution: 2.057→2.131 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.3774 / Mean I/σ(I) obs: 2.01 / Num. unique obs: 5458 / CC1/2: 0.848 / Rpim(I) all: 0.2785 / Rrim(I) all: 0.4722 / % possible all: 79.35

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FTD

5ftd


Resolution: 2.06→29.51 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.917 / SU R Cruickshank DPI: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.19 / SU Rfree Blow DPI: 0.157 / SU Rfree Cruickshank DPI: 0.158
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1995 2.99 %RANDOM
Rwork0.201 ---
obs0.201 66813 97 %-
Displacement parametersBiso mean: 56.27 Å2
Baniso -1Baniso -2Baniso -3
1-7.2829 Å20 Å2-2.4749 Å2
2---2.7674 Å20 Å2
3----4.5155 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2.06→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6768 220 66 496 7550
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017230HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.069860HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2519SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1209HARMONIC5
X-RAY DIFFRACTIONt_it7230HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion18.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion893SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8539SEMIHARMONIC4
LS refinement shellResolution: 2.06→2.08 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2361 -2.84 %
Rwork0.229 1299 -
all0.2292 1337 -
obs--75.11 %
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)
11.4436-0.1106-0.36730.4213-0.25521.5288-0.0378-0.0583-0.1110.0674-0.02050.02940.170.06740.0584-0.1187-0.03210.0105-0.11720.0014-0.165814.0185-36.118173.1031
20.0418-0.93560.70084.28151.06231.0474-0.1386-0.24870.2088-0.07740.05830.0625-0.171-0.09030.0802-0.32410.078-0.086-0.1479-0.19520.10665.4847-89.050654.0412
31.87093.0497-0.42542.4422-2.146-0.05790.00480.0671-0.44780.05090.092-0.07260.5576-0.0113-0.0968-0.01050.0126-0.0151-0.02270.0786-0.028818.198-46.298175.3755
4-0.3646-3.0993.02160.75252.8750.36460.0084-0.0779-0.03640.07280.0120.0325-0.0709-0.0109-0.0205-0.0761-0.0716-0.0683-0.2955-0.16770.2110.6168-81.981760.2766
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ D|* }
4X-RAY DIFFRACTION4{ E|* }

+
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