[English] 日本語
Yorodumi
- PDB-7qsu: Crystal structure of homing endonuclease-associated TliVMA intein... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qsu
TitleCrystal structure of homing endonuclease-associated TliVMA intein (C1A, d333-339)
ComponentsV-ATPase
KeywordsHYDROLASE / intein / protein splicing / endonuclease
Biological speciesThermococcus litoralis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBeyer, H.M. / Iwai, H.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Academy of Finland137995, 277335 Denmark
Novo Nordisk FoundationNNF17OC0025402, NNF17OC0027550 Denmark
CitationJournal: Front Mol Biosci / Year: 2022
Title: Structural Basis for the Propagation of Homing Endonuclease-Associated Inteins.
Authors: Beyer, H.M. / Iwai, H.
History
DepositionJan 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Data collection / Refinement description / Structure summary
Category: refine / reflns / struct
Item: _refine.pdbx_starting_model / _reflns.pdbx_Rmerge_I_obs ..._refine.pdbx_starting_model / _reflns.pdbx_Rmerge_I_obs / _reflns.percent_possible_obs / _struct.title
Revision 1.2Apr 13, 2022Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: V-ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6233
Polymers42,2671
Non-polymers3562
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-8 kcal/mol
Surface area17630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.570, 43.960, 72.120
Angle α, β, γ (deg.)90.000, 104.620, 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 V-ATPase


Mass: 42266.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ...Details: SGKAVDGNTLVLTEEFGLVKIKELYEKLDGKGRKTVEGNEEWTELETPVTVYGYRNGRIVGIKATHIYKGISSGMIEIRTRTGRKIKVTPIHKLFTGRVTKDGLALEEVMAMHIKPGDRIAVVKKIDGGEYVKLTTSPDFRKSRKIKVPEVLDEDLAEFLGYLIADGTLKPRTVAIYNNDESLLKRANFLSTKLFGINGKIVQERTVKALLIHSKPLVDFFRKLGIPESKKARNWKVPRELLLSPPSVVKAFINAYIVCDGYYHERKGEIEITTASEEGAYGLSYLLAKLGIYATFRKKQIKGKEYYRIAISGKTNLEKLGIKRETRGYTNIDIVILFDEVVEVKYIPEPQEVYDITTETHNFVGGNMPTLLHN
Source: (gene. exp.) Thermococcus litoralis (archaea) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM HEPES pH 7.5, 70% (v/v) 2-methyl-2,4-pentanediol (MPD)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→37.2 Å / Num. obs: 33640 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 38.75 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.858 / Net I/σ(I): 19.3
Reflection shellResolution: 1.9→2.01 Å / Num. unique obs: 5361 / CC1/2: 0.793

-
Processing

Software
NameVersionClassification
PHENIX1.15.1_3469refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QSS

7qss


Resolution: 1.9→37.2 Å / SU ML: 0.2023 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.1656
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2102 1682 5 %
Rwork0.1761 31953 -
obs0.1778 33635 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.34 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2915 0 23 114 3052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00823000
X-RAY DIFFRACTIONf_angle_d0.8694044
X-RAY DIFFRACTIONf_chiral_restr0.0616460
X-RAY DIFFRACTIONf_plane_restr0.0054503
X-RAY DIFFRACTIONf_dihedral_angle_d8.15662551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.30021360.26582586X-RAY DIFFRACTION99.42
1.95-2.020.27641390.22582651X-RAY DIFFRACTION99.93
2.02-2.090.25781400.21722643X-RAY DIFFRACTION99.96
2.09-2.170.25951390.2042658X-RAY DIFFRACTION100
2.17-2.270.22651390.18972635X-RAY DIFFRACTION100
2.27-2.390.23431400.18032653X-RAY DIFFRACTION100
2.39-2.540.22871390.18622653X-RAY DIFFRACTION100
2.54-2.740.21621420.18712682X-RAY DIFFRACTION100
2.74-3.010.25861400.18532662X-RAY DIFFRACTION99.96
3.01-3.450.22521400.18122671X-RAY DIFFRACTION100
3.45-4.350.21071420.15462699X-RAY DIFFRACTION99.89
4.35-37.20.16411460.16442760X-RAY DIFFRACTION99.73
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)
12.284200293760.2349613504210.802177441083.40904887351-1.882525881953.345344153390.04066951196910.3950495483660.0845798736228-0.338142344985-0.368475793488-0.3855275244420.1955932832410.6561734533220.2115052221760.2429090728740.04240416921970.03098147448280.3168794748520.05474912091860.31975386182146.6874608297-17.990156102249.9340400848
24.504358224020.1561740700862.677627526561.493180172520.2089846341083.17674273464-0.148528465122-0.08133311709090.5007673210560.0401560149765-0.210350038621-0.0123637763571-0.196138521798-0.2296350023410.3997023012740.3279590039970.01196468625680.04213100198510.236541658223-0.006669689932080.26872581299832.0937036831-19.924041259457.7861924164
34.817369857540.7459810777692.372679807052.947115771330.7719354213454.488578294570.06194304572760.12023720883-0.2742698590470.0188381255286-0.1073742627260.1735549157060.440399512003-0.5451169028360.05134182001220.318225459369-0.02983159308170.02036571428220.407199477401-0.1040075745530.31184758069613.4303513862-29.694055698444.6855580976
43.721437280710.7870605807720.4777056064722.84362069678-0.5149698412493.0908217550.11329229534-0.34858100867-0.06970645005110.334019514919-0.09386131247660.01395898406170.141548967973-0.31663337772-0.02931928337630.27810785996-0.0240111934340.01140818938880.262514956819-0.05115185544110.25327576345926.1646980391-26.349029517862.1889547031
53.72000840824-0.08100710050880.6975472642042.9492952861-2.641936803414.413499423860.1013779775530.218433673037-0.0564201824759-0.0606421161214-0.454780006732-0.4395827739970.03330216026040.6087860027690.2577512229840.3257774750950.003580822766640.006745014375220.286466340421-0.0007653844555580.34380236781247.8531783902-22.501184741457.896507595
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 89 )
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 167 )
3X-RAY DIFFRACTION3chain 'A' and (resid 168 through 235 )
4X-RAY DIFFRACTION4chain 'A' and (resid 236 through 332 )
5X-RAY DIFFRACTION5chain 'A' and (resid 333 through 371 )

+
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