[English] 日本語
Yorodumi
- PDB-4hvx: tRNA-guanine transglycosylase Y106F, C158V mutant in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hvx
TitletRNA-guanine transglycosylase Y106F, C158V mutant in complex with queuine
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTransferase/Transferase Inhibitor / substrate specificity / bacterial TGT / Transferase / guanine exchange enzyme / queuine / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


tRNA-guanosine34 preQ1 transglycosylase / tRNA wobble guanine modification / tRNA-guanosine(34) queuine transglycosylase activity / : / tRNA queuosine(34) biosynthetic process / metal ion binding / cytosol
Similarity search - Function
Queuine tRNA-ribosyltransferase-like / : / tRNA-guanine transglycosylase / tRNA-guanine(15) transglycosylase-like / Queuine tRNA-ribosyltransferase-like / Queuine tRNA-ribosyltransferase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-QEI / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsBiela, I. / Tidten-Luksch, N. / Heine, A. / Reuter, K. / Klebe, G.
CitationJournal: Plos One / Year: 2013
Title: Investigation of Specificity Determinants in Bacterial tRNA-Guanine Transglycosylase Reveals Queuine, the Substrate of Its Eucaryotic Counterpart, as Inhibitor.
Authors: Biela, I. / Tidten-Luksch, N. / Immekus, F. / Glinca, S. / Nguyen, T.X. / Gerber, H.D. / Heine, A. / Klebe, G. / Reuter, K.
History
DepositionNov 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_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: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5256
Polymers42,9061
Non-polymers6195
Water2,972165
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,04912
Polymers85,8112
Non-polymers1,23810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4770 Å2
ΔGint-16 kcal/mol
Surface area24240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.662, 64.486, 71.125
Angle α, β, γ (deg.)90.00, 96.18, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-561-

HOH

21A-632-

HOH

-
Components

#1: Protein Queuine tRNA-ribosyltransferase / Guanine insertion enzyme / tRNA-guanine transglycosylase


Mass: 42905.691 Da / Num. of mol.: 1 / Mutation: Y106F, C158V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis subsp. mobilis (bacteria)
Strain: ATCC 31821 / ZM4 / CP4 / Gene: tgt, ZMO0363 / Plasmid: pET9d-ZM-Y106F_C158V / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE(3) pLysS
References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-QEI / 2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one / queuine


Mass: 277.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15N5O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHR TO LYS CONFLICT AT 312 IN UNP ENTRY P28720

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris, 1 mM DTT, 10% DMSO, 12 % PEG 8000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K

-
Data collection

DiffractionMean temperature: 113.15 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2010 / Details: mirror
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. all: 37328 / Num. obs: 35405 / % possible obs: 94.9 % / Redundancy: 3 % / Biso Wilson estimate: 23.2 Å2 / Rsym value: 0.045 / Net I/σ(I): 21.7
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 1467 / Rsym value: 0.363 / % possible all: 78.4

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GEV

3gev
PDB Unreleased entry


Resolution: 1.82→23.824 Å / SU ML: 0.17 / Isotropic thermal model: TLS / Cross valid method: R-free / σ(F): 1 / Phase error: 20.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1975 3334 9.97 %Random, 10%
Rwork0.1659 ---
obs0.1691 33444 89.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.82→23.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2726 0 32 165 2923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012841
X-RAY DIFFRACTIONf_angle_d1.1583837
X-RAY DIFFRACTIONf_dihedral_angle_d12.7891032
X-RAY DIFFRACTIONf_chiral_restr0.077408
X-RAY DIFFRACTIONf_plane_restr0.005506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.83990.2788940.2196840X-RAY DIFFRACTION61
1.8399-1.86730.23131150.2214983X-RAY DIFFRACTION71
1.8673-1.89650.26161020.20661049X-RAY DIFFRACTION75
1.8965-1.92760.21551220.21541216X-RAY DIFFRACTION84
1.9276-1.96080.20251110.18821158X-RAY DIFFRACTION83
1.9608-1.99640.23851500.1741233X-RAY DIFFRACTION89
1.9964-2.03480.23221380.17871237X-RAY DIFFRACTION90
2.0348-2.07630.19741180.16371337X-RAY DIFFRACTION92
2.0763-2.12140.19271660.16371259X-RAY DIFFRACTION93
2.1214-2.17080.22031560.16041324X-RAY DIFFRACTION94
2.1708-2.2250.21520.15621313X-RAY DIFFRACTION93
2.225-2.28510.21571330.1681293X-RAY DIFFRACTION93
2.2851-2.35230.19251430.15051326X-RAY DIFFRACTION94
2.3523-2.42820.19221560.15571318X-RAY DIFFRACTION95
2.4282-2.51490.20711520.16361288X-RAY DIFFRACTION94
2.5149-2.61540.17441360.16941362X-RAY DIFFRACTION95
2.6154-2.73430.21931370.17191343X-RAY DIFFRACTION95
2.7343-2.87820.20721730.17411303X-RAY DIFFRACTION95
2.8782-3.05820.18951330.16811371X-RAY DIFFRACTION95
3.0582-3.29380.19321420.16671350X-RAY DIFFRACTION95
3.2938-3.62420.16651620.15561311X-RAY DIFFRACTION95
3.6242-4.14630.19511510.14881337X-RAY DIFFRACTION95
4.1463-5.21480.16391390.15161332X-RAY DIFFRACTION93
5.2148-23.8240.22461530.18471227X-RAY DIFFRACTION85
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)
12.4497-0.38040.2010.38040.0391.456-0.0357-0.0581-0.03810.15030.0545-0.0104-0.0323-0.0323-0.00660.17970.01390.0030.12180.00890.18029.19573.214617.831
21.3185-0.4631-0.18761.16580.43491.33690.0446-0.37620.21570.18460.0963-0.1988-0.38960.2007-0.09880.3266-0.0079-0.01810.2256-0.05030.198617.996612.895426.9839
31.0213-0.48431.21670.5182-0.73921.5409-0.07980.1627-0.019-0.00950.0335-0.08840.00350.18010.04840.1591-0.02650.01140.1916-0.01140.196117.79066.6705-1.0196
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 93 )
2X-RAY DIFFRACTION2chain 'A' and (resid 94 through 274 )
3X-RAY DIFFRACTION3chain 'A' and (resid 275 through 383 )

+
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