[English] 日本語
Yorodumi
- PDB-2gj9: Structure of the MnmE G-domain in complex with GDP*AlF4-, Mg2+ and Rb+ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2gj9
TitleStructure of the MnmE G-domain in complex with GDP*AlF4-, Mg2+ and Rb+
ComponentstRNA modification GTPase trmE
KeywordsHYDROLASE / G-domain dimer / alpha-beta-sandwich
Function / homology
Function and homology information


cytosolic tRNA wobble base thiouridylase complex / regulation of cytoplasmic translational fidelity / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / Hydrolases; Acting on acid anhydrides / tRNA wobble uridine modification / tRNA methylation / response to pH / potassium ion binding / chaperone-mediated protein folding / GDP binding ...cytosolic tRNA wobble base thiouridylase complex / regulation of cytoplasmic translational fidelity / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / Hydrolases; Acting on acid anhydrides / tRNA wobble uridine modification / tRNA methylation / response to pH / potassium ion binding / chaperone-mediated protein folding / GDP binding / GTPase activity / GTP binding / protein homodimerization activity / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
tRNA modification GTPase MnmE / GTP-binding protein TrmE, N-terminal / MnmE, helical domain / tRNA modification GTPase MnmE domain 2 / TrmE-type guanine nucleotide-binding domain / GTP-binding protein TrmE N-terminus / MnmE helical domain / TrmE-type guanine nucleotide-binding (G) domain profile. / GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1 / 50S ribosome-binding GTPase ...tRNA modification GTPase MnmE / GTP-binding protein TrmE, N-terminal / MnmE, helical domain / tRNA modification GTPase MnmE domain 2 / TrmE-type guanine nucleotide-binding domain / GTP-binding protein TrmE N-terminus / MnmE helical domain / TrmE-type guanine nucleotide-binding (G) domain profile. / GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1 / 50S ribosome-binding GTPase / GTP binding domain / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / RUBIDIUM ION / tRNA modification GTPase MnmE
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsScrima, A. / Wittinghofer, A.
CitationJournal: Embo J. / Year: 2006
Title: Dimerisation-dependent GTPase reaction of MnmE: how potassium acts as GTPase-activating element.
Authors: Scrima, A. / Wittinghofer, A.
History
DepositionMar 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: tRNA modification GTPase trmE
B: tRNA modification GTPase trmE
C: tRNA modification GTPase trmE
D: tRNA modification GTPase trmE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,10420
Polymers74,4804
Non-polymers2,62416
Water25214
1
A: tRNA modification GTPase trmE
B: tRNA modification GTPase trmE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,55210
Polymers37,2402
Non-polymers1,3128
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: tRNA modification GTPase trmE
D: tRNA modification GTPase trmE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,55210
Polymers37,2402
Non-polymers1,3128
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.240, 70.100, 90.210
Angle α, β, γ (deg.)90.00, 95.76, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit corresponds to a G-domain dimer.

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
tRNA modification GTPase trmE / mnmE


Mass: 18620.121 Da / Num. of mol.: 4 / Fragment: G-domain (216-G384)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Species: Escherichia coli / Strain: BL21DE3 / Gene: trmE, mnmE, thdF / Plasmid: pET14b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P25522

-
Non-polymers , 5 types, 30 molecules

#2: Chemical
ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: AlF4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-RB / RUBIDIUM ION / Rubidium


Mass: 85.468 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Rb
#5: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 16-19% PEG 3350, 100 mM MES pH 6.0, 200 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.815 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 18, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.815 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 48094 / % possible obs: 96.3 % / Biso Wilson estimate: 29.19 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 8.61
Reflection shell
Resolution (Å)Highest resolution (Å)% possible obs (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs
2-2.187.50.2283.41950711255
2.1-2.296.20.1894.82187910283
2.2-2.397.20.156180488457
2.3-2.498.20.1326.7158147347
2.4-2.598.30.1127.5133556190
2.5-398.40.0898.94328620044
3-498.50.05812.13428115856
4-597.40.04814.1121835630
5-698.50.04415.854352515
698.70.03418.357432687

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.864 / SU B: 5.499 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.299 2446 5.1 %RANDOM
Rwork0.25 ---
all0.252 47813 --
obs0.252 47813 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20.06 Å2
2--1.19 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4888 0 140 14 5042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0215088
X-RAY DIFFRACTIONr_angle_refined_deg1.861.9956922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8935638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.50523.519216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.00415876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1741552
X-RAY DIFFRACTIONr_chiral_restr0.1220.2816
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023724
X-RAY DIFFRACTIONr_nbd_refined0.2320.22387
X-RAY DIFFRACTIONr_nbtor_refined0.3050.23401
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2235
X-RAY DIFFRACTIONr_metal_ion_refined0.1150.212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.23
X-RAY DIFFRACTIONr_mcbond_it1.0581.53197
X-RAY DIFFRACTIONr_mcangle_it1.77225118
X-RAY DIFFRACTIONr_scbond_it2.81932049
X-RAY DIFFRACTIONr_scangle_it4.3994.51804
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 188 -
Rwork0.265 3225 -
obs-3413 97.15 %

+
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