[English] 日本語
Yorodumi
- PDB-2ash: Crystal structure of Queuine tRNA-ribosyltransferase (EC 2.4.2.29... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ash
TitleCrystal structure of Queuine tRNA-ribosyltransferase (EC 2.4.2.29) (tRNA-guanine (tm1561) from THERMOTOGA MARITIMA at 1.90 A resolution
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / tm1561 / Queuine tRNA-ribosyltransferase / tRNA-guanine / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


tRNA-guanosine34 preQ1 transglycosylase / tRNA wobble guanine modification / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / queuosine biosynthetic process / metal ion binding / cytoplasm / 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
Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, MOLECULAR REPLACEMENT / molecular replacement/MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Queuine tRNA-ribosyltransferase (EC 2.4.2.29) (tRNA-guanine (tm1561) from THERMOTOGA MARITIMA at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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 / _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_asym_id / _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_asym_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
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Queuine tRNA-ribosyltransferase
B: Queuine tRNA-ribosyltransferase
C: Queuine tRNA-ribosyltransferase
D: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,84123
Polymers171,7824
Non-polymers1,06019
Water11,800655
1
A: Queuine tRNA-ribosyltransferase
B: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,34110
Polymers85,8912
Non-polymers4508
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-31 kcal/mol
Surface area26310 Å2
MethodPISA
2
C: Queuine tRNA-ribosyltransferase
D: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,50013
Polymers85,8912
Non-polymers61011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-26 kcal/mol
Surface area25860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.467, 99.422, 124.163
Angle α, β, γ (deg.)90.000, 123.800, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-455-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: TYR / End label comp-ID: TYR / Auth seq-ID: 2 - 362 / Label seq-ID: 14 - 374

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

-
Components

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


Mass: 42945.410 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: tgt / Production host: Escherichia coli (E. coli) / Strain (production host): DL41
References: UniProt: Q9X1P7, tRNA-guanosine34 preQ1 transglycosylase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 655 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 52.66 %
Crystal growTemperature: 293 K / pH: 10
Details: 15.0% PEG-8000, 0.2M NaCl, 0.1M CHES pH 10.0 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.111
SYNCHROTRONALS 8.3.121.115902, 1.282804
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 2101CCDMar 10, 2004
ADSC QUANTUM 2102CCDFeb 5, 2004KOHZU: double crystal Si(111)
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.1159021
31.2828041
ReflectionResolution: 1.9→51.7 Å / Num. obs: 133817 / % possible obs: 99.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
1.9-1.9599.82.90.6590.499370.659
1.95-299.930.4151.596470.415
2-2.0699.830.3590.793840.359
2.06-2.1299.830.3350.691190.335
2.12-2.1999.730.1863.788050.186
2.19-2.2799.630.2380.885730.238
2.27-2.3699.430.1293.882070.129
2.36-2.4599.23.10.1076.179250.107
2.45-2.5698.93.10.096275290.096
2.56-2.6998.53.10.094.571930.09
2.69-2.8398.13.10.0669.468190.066
2.83-397.93.30.061064450.06
3-3.211004.50.0668.961890.066
3.21-3.471004.50.059857440.059
3.47-3.899.94.50.04712.353210.047
3.8-4.251004.40.04213.548260.042
4.25-4.911004.40.03616.642440.036
4.91-6.0199.94.40.03616.535920.036
6.01-8.599.94.30.03914.728030.039
8.5-51.796.53.90.03915.615150.039

-
Phasing

PhasingMethod: molecular replacement/MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0013refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
autoSHARPphasing
MOLREPphasing
RefinementMethod to determine structure: MAD, MOLECULAR REPLACEMENT
Starting model: 1EFZ

1efz


Resolution: 1.9→51.7 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.909 / SU ML: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.137
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. DENSITY IS WEAK FOR RESIDUES 99-100. NCS WAS USED TO MODEL THIS REGION. (3) RESIDUES 147-148 WERE OMITTED FROM ALL CHAINS DUE TO POOR ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. DENSITY IS WEAK FOR RESIDUES 99-100. NCS WAS USED TO MODEL THIS REGION. (3) RESIDUES 147-148 WERE OMITTED FROM ALL CHAINS DUE TO POOR DENSITY. 4. THE COORDINATION OF ALL FOUR ZINC IONS ARE EQUIVALENT. HOWEVER, THE ENVIRONMENT AROUND THE ZINC ION IN CHAIN D DISTORTS DURING REFINEMENT. THE STRUCTURE WAS INITIALLY SOLVED BY MOLECULAR REPLACEMENT USING THE 1EFZ SEARCH MODEL AND REFINED AGAINST THE 1.9 A NATIVE DATA. DURING REFINEMENT, 2.1 A DATA FROM A MAD EXPERIMENT AT THE ZINC EDGE WERE USED TO CALCULATE EXPERIMENTAL PHASES. THE SUBSTRUCTURE COULD BE SOLVED DE NOVO USING SHELXD AND THE PHASES WERE REFINED WITH AUTOSHARP. THESE PHASES WERE EXTENDED WITH DM USING AMPLITUDES FROM HIGHER RESOLUTION (1.9 A) NATIVE DATA SET. THESE DENSITY MODIFIED ZN-MAD PHASES WERE USED AS RESTRAINTS IN SUBSEQUENT REFINEMENT CYCLES AGAINST THE 1.9 A NATIVE DATA AND WERE INCLUDED IN THE FINAL REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 6626 5 %RANDOM
Rwork0.193 ---
all0.195 ---
obs-124830 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.259 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å2-0.04 Å2
2--0.49 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.9→51.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11070 0 49 655 11774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02211418
X-RAY DIFFRACTIONr_bond_other_d0.0020.027841
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.96415423
X-RAY DIFFRACTIONr_angle_other_deg1.009319086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.19551435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76622.879455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.827151951
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0071578
X-RAY DIFFRACTIONr_chiral_restr0.0940.21770
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212545
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022383
X-RAY DIFFRACTIONr_nbd_refined0.2080.22258
X-RAY DIFFRACTIONr_nbd_other0.1990.28179
X-RAY DIFFRACTIONr_nbtor_refined0.1830.25601
X-RAY DIFFRACTIONr_nbtor_other0.090.26028
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2594
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0030.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1610.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2970.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3290.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.29
X-RAY DIFFRACTIONr_mcbond_it0.9891.57407
X-RAY DIFFRACTIONr_mcbond_other0.2381.52946
X-RAY DIFFRACTIONr_mcangle_it1.475211565
X-RAY DIFFRACTIONr_scbond_it2.45834553
X-RAY DIFFRACTIONr_scangle_it3.6964.53858
Refine LS restraints NCS

Ens-ID: 1 / Number: 4407 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDRmsTypeWeight
1A0.47LOOSE POSITIONAL5
2B0.38LOOSE POSITIONAL5
3C0.35LOOSE POSITIONAL5
4D0.37LOOSE POSITIONAL5
1A2.43LOOSE THERMAL10
2B1.84LOOSE THERMAL10
3C1.44LOOSE THERMAL10
4D1.55LOOSE THERMAL10
LS refinement shellResolution: 1.9→1.944 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 456 -
Rwork0.322 8384 -
obs--88.83 %
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)
12.15450.79740.02840.8351-0.22670.7934-0.2782-0.0931-0.3143-0.0230.08120.1050.2047-0.1770.197-0.03790.00340.1304-0.22020.0045-0.145821.106350.284-16.3454
21.81130.8816-0.07570.9609-0.10281.1514-0.08420.04910.1357-0.04570.0045-0.0901-0.11790.22810.0798-0.154-0.00770.0157-0.13290.0449-0.222152.015776.853-33.0104
33.6053-1.358-1.19291.08790.37631.2952-0.1365-0.34520.94480.10510.2306-0.02450.0455-0.0678-0.0941-0.20320.0545-0.117-0.2016-0.0850.130732.039575.85925.0988
42.7074-1.5434-0.12091.59250.23160.966-0.1412-0.2890.05530.04350.0628-0.2350.0921-0.01780.0784-0.1930.077-0.0331-0.12510.0484-0.176967.112548.889423.8152
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: all

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 36313 - 375
22BB2 - 36214 - 374
33CC1 - 36313 - 375
44DD1 - 36313 - 375

+
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