[English] 日本語
Yorodumi
- PDB-6nl1: Structure of T. brucei MERS1 protein in its apo form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nl1
TitleStructure of T. brucei MERS1 protein in its apo form
ComponentsMitochondrial edited mRNA stability factor 1
KeywordsRNA BINDING PROTEIN / MERS1 / mRNA processing / nudix
Function / homologyNUDIX domain / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Mitochondrial edited mRNA stability factor 1
Function and homology information
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.297 Å
AuthorsSchumacher, M.A.
CitationJournal: Rna / Year: 2020
Title: Structures of MERS1, the 5' processing enzyme of mitochondrial mRNAs inTrypanosoma brucei.
Authors: Schumacher, M.A. / Henderson, M. / Zeng, W.
History
DepositionJan 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mitochondrial edited mRNA stability factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0985
Polymers44,7141
Non-polymers3844
Water4,468248
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Mitochondrial edited mRNA stability factor 1
hetero molecules

A: Mitochondrial edited mRNA stability factor 1
hetero molecules

A: Mitochondrial edited mRNA stability factor 1
hetero molecules

A: Mitochondrial edited mRNA stability factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,39420
Polymers178,8574
Non-polymers1,53716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area10900 Å2
ΔGint-262 kcal/mol
Surface area50570 Å2
MethodPISA
3
A: Mitochondrial edited mRNA stability factor 1
hetero molecules

A: Mitochondrial edited mRNA stability factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,19710
Polymers89,4282
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Buried area4160 Å2
ΔGint-121 kcal/mol
Surface area26570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.160, 122.160, 170.101
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-573-

HOH

21A-743-

HOH

-
Components

#1: Protein Mitochondrial edited mRNA stability factor 1


Mass: 44714.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: MERS1 / Production host: Escherichia coli (E. coli) / References: UniProt: B6SBM0
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 4.1 Å3/Da / Density % sol: 69.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.6 M Magnesium sulphate, 0.1 M HEPES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Dec 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.297→49.975 Å / Num. obs: 33970 / % possible obs: 99.7 % / Redundancy: 5 % / CC1/2: 0.997 / Rpim(I) all: 0.028 / Rsym value: 0.45 / Net I/σ(I): 13
Reflection shellResolution: 2.2975→2.356 Å / CC1/2: 0.879 / Rpim(I) all: 0.278 / Rsym value: 0.345

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.297→49.975 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.03
RfactorNum. reflection% reflection
Rfree0.2131 1718 5.06 %
Rwork0.1875 --
obs0.1889 33970 99.73 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Bsol: 48.741 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 155.59 Å2 / Biso mean: 40.14 Å2 / Biso min: 15.83 Å2
Baniso -1Baniso -2Baniso -3
1-3.1514 Å20 Å2-0 Å2
2--3.1514 Å20 Å2
3----6.3027 Å2
Refinement stepCycle: final / Resolution: 2.297→49.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2151 0 20 248 2419
Biso mean--87.95 48.25 -
Num. residues----262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072228
X-RAY DIFFRACTIONf_angle_d1.0173037
X-RAY DIFFRACTIONf_chiral_restr0.071320
X-RAY DIFFRACTIONf_plane_restr0.004386
X-RAY DIFFRACTIONf_dihedral_angle_d12.715827
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2974-2.37950.30211630.2463127329099
2.3795-2.47480.23551690.223531603329100
2.4748-2.58740.25331620.218331853347100
2.5874-2.72380.23781510.214931863337100
2.7238-2.89440.23761850.193531843369100
2.8944-3.11790.22551770.188831833360100
3.1179-3.43160.20281850.18232053390100
3.4316-3.9280.18861480.169332643412100
3.928-4.94810.16761900.147332663456100
4.9481-49.98710.23681880.2134923680100
Refinement TLS params.Method: refined / Origin x: 61.3837 Å / Origin y: -15.6503 Å / Origin z: 16.1326 Å
111213212223313233
T0.2134 Å20.0287 Å2-0.0161 Å2-0.1363 Å20.0175 Å2--0.1549 Å2
L0.5216 °20.2462 °20.2257 °2-0.4035 °2-0.0651 °2--0.5173 °2
S0.0469 Å °-0.046 Å °-0.0921 Å °0.0444 Å °-0.0368 Å °0.0085 Å °0.0992 Å °-0.0146 Å °-0.0002 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA77 - 353
2X-RAY DIFFRACTION1allT122 - 125
3X-RAY DIFFRACTION1allS1 - 248

+
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