[English] 日本語
Yorodumi
- PDB-9ky9: Crystal structure of E. coli tryptophanyl-tRNA synthetase complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ky9
TitleCrystal structure of E. coli tryptophanyl-tRNA synthetase complexed with 3-methylchuangxinmycin and tryptophanyl-5'-AMP
ComponentsTryptophan--tRNA ligase
KeywordsLIGASE / tryptophanyl-tRNA synthetase / aminoacyl-tRNA synthetase / antibiotic
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophanyl-tRNA aminoacylation / tryptophan-tRNA ligase activity / ATP binding / cytosol
Similarity search - Function
Tryptophan-tRNA ligase, bacterial-type / : / Tryptophan-tRNA ligase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
: / TRYPTOPHANYL-5'AMP / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsRen, Y. / Wang, S. / Liu, W. / Fang, P.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2303100 China
CitationJournal: Rsc Chem Biol / Year: 2025
Title: Mechanistic insights into the ATP-mediated and species-dependent inhibition of TrpRS by chuangxinmycin.
Authors: Ren, Y. / Wang, S. / Liu, W. / Wang, J. / Fang, P.
History
DepositionDec 8, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tryptophan--tRNA ligase
B: Tryptophan--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6006
Polymers76,6272
Non-polymers9734
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6790 Å2
ΔGint-68 kcal/mol
Surface area26520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.761, 90.851, 74.753
Angle α, β, γ (deg.)90.000, 109.472, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Tryptophan--tRNA ligase / Tryptophanyl-tRNA synthetase / TrpRS


Mass: 38313.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: trpS, ACU57_16550, B6R15_000448, B6R31_002275, BANRA_02015, BCB93_002501, BGM66_002290, BGZ_04191, BK383_21195, BKL28_001915, BMT91_03555, BvCmsNSP007_00090, BXT93_04920, C0P57_000786, C2R31_ ...Gene: trpS, ACU57_16550, B6R15_000448, B6R31_002275, BANRA_02015, BCB93_002501, BGM66_002290, BGZ_04191, BK383_21195, BKL28_001915, BMT91_03555, BvCmsNSP007_00090, BXT93_04920, C0P57_000786, C2R31_002885, C3F40_19370, CG704_07870, CIG67_21025, CTR35_001866, D9D43_04205, DD762_12005, DL968_00250, DNQ45_04190, DTL43_13995, DU321_12325, E4K51_10330, E6D34_04225, EIA08_11870, EPS97_04620, F7F11_12075, F7N46_14665, F9413_17445, F9461_03030, F9B07_12605, FGAF848_25410, FKO60_13960, FOI11_018845, FOI11_04335, FPS11_03390, FZU14_04195, G3V95_06005, G4A38_16925, G4A47_18515, G5603_11025, GAI89_06310, GNW61_08470, GOP25_12480, GP944_08250, GQE86_01825, GQN24_10725, HEP34_002452, HI055_002233, HJQ60_002846, HL563_11055, HL601_09110, HLX92_09755, HLZ50_06610, HMV95_07850, HVW04_17215, HVW43_18350, HVY77_01760, I6H00_19775, IH772_08800, J0541_002134, JNP96_25720, NCTC10764_03793, NCTC10974_00460, NCTC9044_01447, NCTC9073_00479, NCTC9077_00527, NCTC9706_02656, P6223_000209, Q2V20_09290, QDW62_01780, QO046_14075, R8G00_13645, SAMEA3472044_01080, SAMEA3472056_01981, SAMEA3752557_02035
Production host: Escherichia coli (E. coli) / References: UniProt: E2QFN4, tryptophan-tRNA ligase
#2: Chemical ChemComp-A1EHN / (6~{R})-5,5-dimethyl-7-thia-2-azatricyclo[6.3.1.0^{4,12}]dodeca-1(12),3,8,10-tetraene-6-carboxylic acid / Meloxicam


Mass: 247.313 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H13NO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TYM / TRYPTOPHANYL-5'AMP


Mass: 533.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N7O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.33 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium sulfate, 0.1 M MES, 20% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.19→70.48 Å / Num. obs: 40144 / % possible obs: 100 % / Redundancy: 6.1 % / Biso Wilson estimate: 28.55 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 8
Reflection shellResolution: 2.19→2.25 Å / Rmerge(I) obs: 0.489 / Num. unique obs: 2936

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8I1W

8i1w


Resolution: 2.19→70.48 Å / SU ML: 0.2772 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.823
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2369 1993 5.03 %
Rwork0.2081 37667 -
obs0.2095 39660 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.74 Å2
Refinement stepCycle: LAST / Resolution: 2.19→70.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5110 0 64 236 5410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00835279
X-RAY DIFFRACTIONf_angle_d0.99377163
X-RAY DIFFRACTIONf_chiral_restr0.0528796
X-RAY DIFFRACTIONf_plane_restr0.008941
X-RAY DIFFRACTIONf_dihedral_angle_d5.8715761
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.240.51341370.47842457X-RAY DIFFRACTION91.63
2.24-2.310.41491450.39982627X-RAY DIFFRACTION96.92
2.31-2.370.29061310.2442731X-RAY DIFFRACTION99.65
2.37-2.450.26171470.21882681X-RAY DIFFRACTION99.37
2.45-2.540.27021470.21622682X-RAY DIFFRACTION99.79
2.54-2.640.28621420.2192706X-RAY DIFFRACTION99.86
2.64-2.760.28941420.25042696X-RAY DIFFRACTION98.82
2.76-2.90.27871460.23312709X-RAY DIFFRACTION99.79
2.9-3.090.27711420.21812733X-RAY DIFFRACTION100
3.09-3.320.21241450.20662700X-RAY DIFFRACTION100
3.33-3.660.20171450.19842734X-RAY DIFFRACTION99.31
3.66-4.190.19871420.17942711X-RAY DIFFRACTION99.41
4.19-5.280.18571380.1482746X-RAY DIFFRACTION99.97
5.28-70.480.15961440.16042754X-RAY DIFFRACTION98.74

+
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