[English] 日本語
Yorodumi
- PDB-6s3n: Crystal structure of helicase Pif1 from Thermus oshimai in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6s3n
TitleCrystal structure of helicase Pif1 from Thermus oshimai in complex with ssDNA (dT)18 and ADP-VO4
Components
  • (DNA (5'-D(P*TP*TP*TP*TP*TP*T)- ...) x 2
  • PIF1 helicase
KeywordsHYDROLASE / DNA helicase
Function / homology
Function and homology information


DNA helicase activity / telomere maintenance / DNA repair
Similarity search - Function
DNA helicase Pif1-like / PIF1-like helicase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / VANADATE ION / DNA / DNA (> 10) / PIF1 helicase
Similarity search - Component
Biological speciesThermus oshimai (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.533 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
C: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
D: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,90110
Polymers111,7684
Non-polymers1,1336
Water63135
1
A: PIF1 helicase
C: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4385
Polymers55,8712
Non-polymers5663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-36 kcal/mol
Surface area19310 Å2
MethodPISA
2
B: PIF1 helicase
D: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4635
Polymers55,8962
Non-polymers5663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-35 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.093, 102.955, 249.697
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1116-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#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 (bacteria) / Gene: Theos_1468 / Plasmid: pET15b-SUMO / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): C2566H / References: UniProt: K7RJ88

-
DNA (5'-D(P*TP*TP*TP*TP*TP*T)- ... , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')


Mass: 5430.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus oshimai (bacteria)
#3: DNA chain DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')


Mass: 5455.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus oshimai (bacteria)

-
Non-polymers , 4 types, 41 molecules

#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#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: Chemical ChemComp-VO4 / VANADATE ION / Vanadate


Mass: 114.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Osdium Hepes-MOPS 0.1M NaF 0.03M NaI 0.03M NaBr 0.03M PEG 4K 20% Glycerol 20%

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.533→44.05 Å / Num. obs: 36510 / % possible obs: 95.51 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 55.47 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.1217 / Rpim(I) all: 0.0493 / Rrim(I) all: 0.1315 / Net I/σ(I): 10.44
Reflection shellResolution: 2.533→2.624 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.7295 / Mean I/σ(I) obs: 2.26 / Num. unique obs: 3756 / CC1/2: 0.929 / Rpim(I) all: 0.2652 / Rrim(I) all: 0.7838 / Χ2: 0.929 / % possible all: 99.71

-
Processing

Software
NameVersionClassification
PHENIX(1.14rc1_3177: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FTD

5ftd


Resolution: 2.533→44.047 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.86
RfactorNum. reflection% reflectionSelection details
Rfree0.2553 1782 4.89 %5%
Rwork0.1982 ---
obs0.201 36464 95.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.533→44.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7008 208 66 35 7317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037466
X-RAY DIFFRACTIONf_angle_d0.77310184
X-RAY DIFFRACTIONf_dihedral_angle_d24.2462846
X-RAY DIFFRACTIONf_chiral_restr0.0461122
X-RAY DIFFRACTIONf_plane_restr0.0051284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5335-2.6020.32881500.28232759X-RAY DIFFRACTION100
2.602-2.67850.37141100.28852026X-RAY DIFFRACTION74
2.6785-2.7650.38271250.27362703X-RAY DIFFRACTION98
2.765-2.86380.32471550.2642761X-RAY DIFFRACTION100
2.8638-2.97840.35111500.24412732X-RAY DIFFRACTION100
2.9784-3.11390.27951260.24372784X-RAY DIFFRACTION100
3.1139-3.2780.29211360.23442786X-RAY DIFFRACTION100
3.278-3.48330.30311030.23032201X-RAY DIFFRACTION79
3.4833-3.75220.24621480.20622557X-RAY DIFFRACTION92
3.7522-4.12950.25171450.1912770X-RAY DIFFRACTION100
4.1295-4.72640.21821640.15372812X-RAY DIFFRACTION100
4.7264-5.95250.22541330.17262841X-RAY DIFFRACTION100
5.9525-44.05310.20671370.16832950X-RAY DIFFRACTION99
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)
10.77040.1158-0.9020.5101-0.08581.474-0.01040.30130.1072-0.0013-0.0023-0.13460.06870.0556-00.46980.0282-0.0160.7032-0.02140.540729.855-1.2233-59.956
20.8373-0.4053-0.14661.2893-0.38771.02970.0362-0.52250.04890.44590.0156-0.5180.18410.4186-00.47750.0628-0.07310.7262-0.10520.718440.91240.6785-40.261
30.9191-0.54090.73742.02060.22250.8403-0.03610.1390.3038-0.04670.0354-0.0848-0.13240.154600.45620.0054-0.0170.6405-0.08860.544135.09216.5391-48.045
40.8553-0.4793-0.17520.76170.56830.4207-0.0303-0.03040.5718-0.0323-0.0044-0.1885-0.354-0.30100.52620.002-0.02140.6404-0.06860.734331.076115.0338-47.0816
52.3395-0.18380.76331.51910.13662.9801-0.03430.24660.1936-0.09550.17720.20660.0333-0.1557-00.46720.0335-0.00150.6145-0.04420.58624.90781.5301-53.8694
62.1084-0.61580.47211.9612-0.04571.65040.0215-0.24340.03550.250.1004-0.10020.0699-0.1362-00.55290.01320.01360.6100.517420.39-8.5856-32.0367
73.007-1.0377-0.55391.0240.05072.53210.1165-0.07010.47040.1574-0.2252-0.0219-0.41080.0073-00.48550.0689-0.02240.5852-0.0370.613413.71319.7606-49.8356
80.48740.04350.0850.4669-0.22950.2010.0219-0.6795-0.49990.83930.23950.02150.62260.4618-01.18440.2036-0.1650.76240.07490.62445.4537-30.66130.8319
91.8771-0.357-0.32670.92540.30551.8185-0.068-0.3891-0.57660.37180.19330.04550.614-0.078300.93310.0678-0.09410.50530.07530.737541.6026-39.0646-16.5
102.0838-0.94250.61291.09320.06990.93150.1207-0.3598-0.47060.54090.10290.4542-0.002-0.62070.00010.8958-0.05270.02550.55750.08370.648432.734-30.773-12.4639
110.79780.17020.25832.22721.24341.71970.0908-0.66130.54530.16940.1527-0.1103-0.18830.174-00.77410.0945-0.08220.6631-0.17290.677847.6057-5.6831-7.9506
121.44920.0522-0.63122.57880.96951.85230.0787-0.1892-0.119-0.1060.187-0.2808-0.46090.291800.73510.0070.00790.6355-0.12080.733959.0877-21.1192-30.1726
131.5-1.1889-0.66851.9760.93852.26350.04610.1261-0.06580.00050.1756-0.22750.16480.0161-00.67620.0349-0.04290.5573-0.11210.601951.0727-26.106-27.4659
140.7977-1.22490.22322.99020.44172.1221-0.2355-0.25770.2010.2870.36180.515-0.0138-0.3129-00.78320.0664-0.05880.63280.01250.67538.1045-13.1968-11.4595
150.59340.59450.06690.7376-0.23730.6594-0.603-0.66660.62520.99140.0732-0.34610.0534-0.051300.78050.1058-0.11290.8639-0.02380.606822.81091.4071-34.9002
160.71320.60440.27820.52070.32630.8438-0.06591.1397-0.2907-0.2437-0.43370.149-0.10890.351200.78630.0047-0.13330.6022-0.02080.695344.7962-24.3633-25.8325
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 68 through 125 )
2X-RAY DIFFRACTION2chain 'A' and (resid 126 through 165 )
3X-RAY DIFFRACTION3chain 'A' and (resid 166 through 221 )
4X-RAY DIFFRACTION4chain 'A' and (resid 222 through 252 )
5X-RAY DIFFRACTION5chain 'A' and (resid 253 through 303 )
6X-RAY DIFFRACTION6chain 'A' and (resid 304 through 446 )
7X-RAY DIFFRACTION7chain 'A' and (resid 447 through 502 )
8X-RAY DIFFRACTION8chain 'B' and (resid 68 through 119 )
9X-RAY DIFFRACTION9chain 'B' and (resid 120 through 193 )
10X-RAY DIFFRACTION10chain 'B' and (resid 194 through 252 )
11X-RAY DIFFRACTION11chain 'B' and (resid 253 through 303 )
12X-RAY DIFFRACTION12chain 'B' and (resid 304 through 374 )
13X-RAY DIFFRACTION13chain 'B' and (resid 375 through 446 )
14X-RAY DIFFRACTION14chain 'B' and (resid 447 through 502 )
15X-RAY DIFFRACTION15chain 'C' and (resid 3 through 8 )
16X-RAY DIFFRACTION16chain 'D' and (resid 3 through 8 )

+
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