[English] 日本語
Yorodumi
- PDB-8apt: Crystal Structure of H. influenzae TrmD in complex with Compound 13 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8apt
TitleCrystal Structure of H. influenzae TrmD in complex with Compound 13
ComponentstRNA (guanine-N(1)-)-methyltransferase
KeywordsRNA BINDING PROTEIN / Methyltransferase
Function / homology
Function and homology information


tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / tRNA modification / methylation / cytoplasm
Similarity search - Function
tRNA (guanine-N1-)-methyltransferase, bacteria / tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases
Similarity search - Domain/homology
CITRIC ACID / Chem-NN9 / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHall, G. / Cowan, R. / Carr, M.D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other government United Kingdom
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2023
Title: Evaluating the druggability of TrmD, a potential antibacterial target, through design and microbiological profiling of a series of potent TrmD inhibitors.
Authors: Wilkinson, A.J. / Ooi, N. / Finlayson, J. / Lee, V.E. / Lyth, D. / Maskew, K.S. / Newman, R. / Orr, D. / Ansell, K. / Birchall, K. / Canning, P. / Coombs, P. / Fusani, L. / McIver, E. / ...Authors: Wilkinson, A.J. / Ooi, N. / Finlayson, J. / Lee, V.E. / Lyth, D. / Maskew, K.S. / Newman, R. / Orr, D. / Ansell, K. / Birchall, K. / Canning, P. / Coombs, P. / Fusani, L. / McIver, E. / Pisco, J. / Ireland, P.M. / Jenkins, C. / Norville, I.H. / Southern, S.J. / Cowan, R. / Hall, G. / Kettleborough, C. / Savage, V.J. / Cooper, I.R.
History
DepositionAug 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 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: tRNA (guanine-N(1)-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1983
Polymers29,7501
Non-polymers4482
Water7,494416
1
A: tRNA (guanine-N(1)-)-methyltransferase
hetero molecules

A: tRNA (guanine-N(1)-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3976
Polymers59,5002
Non-polymers8974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area7500 Å2
ΔGint-29 kcal/mol
Surface area22920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.671, 94.671, 177.958
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-615-

HOH

21A-654-

HOH

31A-742-

HOH

41A-773-

HOH

51A-794-

HOH

61A-812-

HOH

71A-816-

HOH

-
Components

#1: Protein tRNA (guanine-N(1)-)-methyltransferase / M1G-methyltransferase / tRNA [GM37] methyltransferase


Mass: 29750.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: PittGG / Gene: trmD, CGSHiGG_03625 / Production host: Escherichia coli (E. coli)
References: UniProt: A5UG04, tRNA (guanine37-N1)-methyltransferase
#2: Chemical ChemComp-NN9 / 6-[[3-(aminomethyl)phenyl]methylamino]pyridine-3-carboxamide


Mass: 256.303 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16N4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG3350 0.1 M HEPES, pH 7.5 0.1 M potassium citrate tribasic

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→47.38 Å / Num. obs: 28700 / % possible obs: 99.8 % / Redundancy: 10.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.075 / Rrim(I) all: 0.174 / Net I/σ(I): 14.9
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.186 / Num. unique obs: 1639 / CC1/2: 0.559 / Rpim(I) all: 0.643 / Rrim(I) all: 1.357

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
StructureStudiodata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YVH

4yvh


Resolution: 1.8→47.38 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.287 / SU ML: 0.069 / Cross valid method: FREE R-VALUE / ESU R: 0.116 / ESU R Free: 0.102
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1794 2931 10.213 %
Rwork0.1613 25767 -
all0.163 --
obs-28698 99.805 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.697 Å2
Baniso -1Baniso -2Baniso -3
1-0.002 Å20.001 Å20 Å2
2--0.002 Å20 Å2
3----0.006 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1947 0 32 416 2395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0132027
X-RAY DIFFRACTIONr_bond_other_d0.0020.0151947
X-RAY DIFFRACTIONr_angle_refined_deg1.8471.6432742
X-RAY DIFFRACTIONr_angle_other_deg1.5211.5824489
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5345248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57721.524105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01915354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9951516
X-RAY DIFFRACTIONr_chiral_restr0.1080.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022265
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02450
X-RAY DIFFRACTIONr_nbd_refined0.2310.2424
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.21785
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2972
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.2921
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.330.2302
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.090.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1890.225
X-RAY DIFFRACTIONr_nbd_other0.2520.2111
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4120.255
X-RAY DIFFRACTIONr_mcbond_it2.1581.62992
X-RAY DIFFRACTIONr_mcbond_other2.1471.618991
X-RAY DIFFRACTIONr_mcangle_it2.9312.4161237
X-RAY DIFFRACTIONr_mcangle_other2.9312.4191238
X-RAY DIFFRACTIONr_scbond_it3.3381.9331035
X-RAY DIFFRACTIONr_scbond_other3.3191.9291032
X-RAY DIFFRACTIONr_scangle_it4.8992.7571504
X-RAY DIFFRACTIONr_scangle_other4.8972.7591505
X-RAY DIFFRACTIONr_lrange_it11.21822.8762466
X-RAY DIFFRACTIONr_lrange_other10.66720.8552299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.2942050.2831830X-RAY DIFFRACTION97.6956
1.847-1.8970.2541830.2311868X-RAY DIFFRACTION99.9513
1.897-1.9520.2142200.2081776X-RAY DIFFRACTION100
1.952-2.0120.1992130.1821742X-RAY DIFFRACTION100
2.012-2.0780.2122140.181650X-RAY DIFFRACTION100
2.078-2.1510.1881480.1621669X-RAY DIFFRACTION100
2.151-2.2320.1651830.1531576X-RAY DIFFRACTION100
2.232-2.3230.1631730.1491497X-RAY DIFFRACTION100
2.323-2.4270.1781910.1451455X-RAY DIFFRACTION100
2.427-2.5450.1511600.1471391X-RAY DIFFRACTION100
2.545-2.6820.1591610.1471321X-RAY DIFFRACTION100
2.682-2.8450.171390.1461273X-RAY DIFFRACTION100
2.845-3.0410.1781390.1581183X-RAY DIFFRACTION100
3.041-3.2840.1651200.1551124X-RAY DIFFRACTION100
3.284-3.5970.1581020.1491037X-RAY DIFFRACTION100
3.597-4.020.1571220.131922X-RAY DIFFRACTION100
4.02-4.640.175790.13840X-RAY DIFFRACTION100
4.64-5.6770.148850.14714X-RAY DIFFRACTION100
5.677-8.0060.262640.195554X-RAY DIFFRACTION100
8.006-47.380.151300.194345X-RAY DIFFRACTION98.1675

+
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