[English] 日本語
Yorodumi
- PDB-7ada: Crystal structure of helicase Pif1 from Thermus oshimai mutant Q1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ada
TitleCrystal structure of helicase Pif1 from Thermus oshimai mutant Q164C-E409C
ComponentsPIF1 helicase
KeywordsHYDROLASE / DNA helicase
Function / homology
Function and homology information


DNA helicase activity / telomere maintenance / 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
Biological speciesThermus oshimai JL-2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.34 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 China (NSFC)31370798,11304252,11574252,31301632 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
DepositionSep 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 31, 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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PIF1 helicase
B: PIF1 helicase


Theoretical massNumber of molelcules
Total (without water)101,2082
Polymers101,2082
Non-polymers00
Water00
1
A: PIF1 helicase


Theoretical massNumber of molelcules
Total (without water)50,6041
Polymers50,6041
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PIF1 helicase


Theoretical massNumber of molelcules
Total (without water)50,6041
Polymers50,6041
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.070, 58.679, 118.155
Angle α, β, γ (deg.)90.000, 92.208, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein PIF1 helicase


Mass: 50604.141 Da / Num. of mol.: 2 / Mutation: Q164C, E409C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus oshimai JL-2 (bacteria) / Gene: Theos_1468
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: K7RJ88
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 0.1 M Sodium Hepes-MOPS (pH 7.5) 0.03 M CaCl2 0.03 M MgCl2 10% PEG8000 20% ethylene glycol.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97891 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 3.34→52.55 Å / Num. obs: 15002 / % possible obs: 99.58 % / Redundancy: 6.9 % / Biso Wilson estimate: 138.11 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.0492 / Rpim(I) all: 0.0209 / Rrim(I) all: 0.05357 / Net I/σ(I): 24.54
Reflection shellResolution: 3.34→3.46 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.5995 / Mean I/σ(I) obs: 2.79 / Num. unique obs: 1501 / CC1/2: 0.922 / CC star: 0.979 / Rpim(I) all: 0.2415 / Rrim(I) all: 0.647 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSMar 15, 2019, built on 20191211data reduction
Aimless0.7.4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S3E

6s3e


Resolution: 3.34→52.55 Å / SU ML: 0.5092 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 37.7776
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3016 754 5.04 %
Rwork0.2447 14220 -
obs0.2477 14974 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 166.27 Å2
Refinement stepCycle: LAST / Resolution: 3.34→52.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6996 0 0 0 6996
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047162
X-RAY DIFFRACTIONf_angle_d0.87679718
X-RAY DIFFRACTIONf_chiral_restr0.04791070
X-RAY DIFFRACTIONf_plane_restr0.00481266
X-RAY DIFFRACTIONf_dihedral_angle_d20.23492720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.34-3.60.45161410.36792821X-RAY DIFFRACTION99.66
3.6-3.960.41551460.31762823X-RAY DIFFRACTION99.46
3.96-4.530.31541740.27912797X-RAY DIFFRACTION99.6
4.53-5.710.36951500.25482859X-RAY DIFFRACTION99.9
5.71-52.550.2241430.20012920X-RAY DIFFRACTION99.45
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)
10.459529685542-0.1973239997080.4176335848040.6819087699370.1169745555960.860257242473-0.5849637533030.2415092209440.2976975323440.3574776808330.477230436296-0.264875872203-0.2858117690262.40487792270.003508545940191.455304169660.351010391295-0.1792611656831.670169919340.1413535547661.33528385857-14.4084632859-0.20547190735919.5845160526
21.66044753982-0.1395357100211.855489986713.161067817470.422295898951.995631880540.156748686324-0.392459071333-0.0230640348719-0.6337133243350.2514049308950.3009879199330.412514589226-0.3901904576272.62764331352E-51.21897164369-0.0695368355573-0.1791018701481.116737757220.1438342540820.901160362811-34.49901244010.97649465373714.6236386942
31.03869188099-0.847078826987-0.4148754399961.254914974641.386845055622.019354111140.171724074297-0.162454440998-0.83053415739-0.1800074597480.796056921010.1422100055551.02406310687-0.709652438072-0.0001208848964011.50272619053-0.236834296625-0.3625544373881.145494539610.238253958551.42445036636-30.66556129973.703145557222.0624665946
40.2907954362690.5553110556260.08462160135010.759789411039-0.008240904648150.009866060016860.155520140059-0.633926597025-0.3962853030790.1725421094210.04356870410010.3683086609840.328560173932-0.354895792839.76741278208E-51.30772346328-0.0292279288362-0.1517756832291.428056518790.01939953824251.21442722356-26.126724056111.151430539926.8683058653
51.915719958540.516027705330.0512677208411.354788130711.072879218380.904964802792-0.3660991837610.2312799818951.47044325760.146747069551-0.354895857836-0.312445368857-0.537845847413-0.343342612456-0.001041951216151.07161303954-0.0100002384198-0.1316760879361.099505523550.08566075445441.35795415387-12.795262708331.98099947622.1164925409
60.581108219736-0.366226739302-0.2031153255510.323066021441-0.01325045153560.234113989781-0.690997886311.24036438580.0426916778667-1.518165285260.498872005643-0.2591518937350.01531359796290.3911910765950.0006039900176441.52250752974-0.212594585111-0.2267356777861.869616842390.06082026327961.37470371191-18.147239679326.0870517761-6.26806790885
70.04995286608780.27202707097-0.1503292173671.28437587119-1.14851427170.888436098105-0.204122077530.440964016585-0.598647802942-0.5542648255120.342570896484-0.911123872710.829780605050.2775827095710.0001709716874791.318886683630.1592096181360.140631454611.97379876038-0.1310622574661.5447385295-9.9280283295216.7900139519-3.30484207049
80.135576014830.5907602680110.3997852338740.5536426317760.6151076500571.10923945059-0.1906772176960.1130427901860.10941239277-1.23386083217-0.510066355478-1.588301313870.5430121843460.4754642235590.001273973186691.5811241455-0.1162526711130.02936736672621.69552416516-0.0160938750331.19912800549-22.5342629433.749194753320.651350953429
90.4941716786010.5167543987330.02365431044260.4584621438540.2119676836831.62469780012-0.408625554253-0.330823665502-0.00184373039883-0.6623793291530.5074913333490.3566997781050.279133657746-0.170898629225-3.59585587746E-51.26000433972-0.0124721801630.1411724236051.272736430620.06930188770011.51823096921-17.136919102328.419046095618.261068811
100.356374001455-0.0758001794984-0.4225506323670.4137916846850.2205063908130.5206241304230.182775216505-3.067484291010.08562006365120.758804640190.54584310105-1.11732883153-0.1137650622080.1862568735070.03721361481621.46374367793-0.111952944759-0.4010885386041.227767225770.2307547570781.16647003013-25.141375285611.297649229734.1625687022
110.2572458217510.193308588783-0.08296283609760.633574932367-0.6745500722610.710114125592-0.3394262038242.576403813250.062668284584-1.01784754738-0.2251201135911.547971323970.0528814691721-2.333024418180.002939648381911.988376807130.305106662331-0.2837088504172.099115931110.3676903455042.23789009909-65.3379688312-1.2512066389136.0254602838
124.3903411088-1.789160897352.480658068111.572879570880.2806449211512.41454108678-0.1540896397930.2165485485210.428851711250.5547990645260.348051148853-0.429531438438-0.09191661252360.6525237463230.0003137227271461.48435114416-0.2697832445470.4710047656350.863222693916-0.3452372300761.84327975941-59.9839894524-4.0312887563254.9046409727
130.0514499816231-0.316817477225-0.4348186588710.8947466285141.234841290931.154899417820.199458747010.4404128659780.158071287420.82729131914-0.6213300827420.8125764768630.788260073915-1.5559298904-0.001104738069691.61117094642-0.1590216660160.03124883913711.62032242678-0.01504164383512.07742349634-71.8960261678-9.2325354605543.9776475911
143.66334477083-0.135726013451.08873738432.607390609740.2389856887970.290146525222-0.000391550714788-0.302060465750.283679213321-0.06257178077570.0730448873347-0.2925746597920.1431279821640.526091469929-0.003720502790391.10107803508-0.01043785629560.05811276421991.36093741508-0.1803288596520.931601311046-51.0410786676-24.786829978138.9031031409
151.503126961420.3562729657441.510906105282.112275243381.254306264361.65562397471-0.1296687851890.1272065536090.4342063105330.123862280639-0.09577638445770.4347193478470.13762538826-0.430364307267-0.0002412308833371.037469126530.01106523120370.1013062725520.988552740563-0.05106139308891.42745857619-70.8733112174-23.962722249443.9566226913
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 67 through 107 )AA67 - 1071 - 41
22chain 'A' and (resid 108 through 190 )AA108 - 19042 - 124
33chain 'A' and (resid 191 through 220 )AA191 - 220125 - 154
44chain 'A' and (resid 221 through 260 )AA221 - 260155 - 194
55chain 'A' and (resid 261 through 302 )AA261 - 302195 - 236
66chain 'A' and (resid 303 through 330 )AA303 - 330237 - 264
77chain 'A' and (resid 331 through 393 )AA331 - 393265 - 327
88chain 'A' and (resid 394 through 430 )AA394 - 430328 - 364
99chain 'A' and (resid 431 through 483 )AA431 - 483365 - 417
1010chain 'A' and (resid 484 through 502 )AA484 - 502418 - 436
1111chain 'B' and (resid 67 through 96 )BB67 - 961 - 30
1212chain 'B' and (resid 97 through 229 )BB97 - 22931 - 163
1313chain 'B' and (resid 230 through 260 )BB230 - 260164 - 194
1414chain 'B' and (resid 261 through 430 )BB261 - 430195 - 364
1515chain 'B' and (resid 431 through 502 )BB431 - 502365 - 436

+
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