[English] 日本語
Yorodumi
- PDB-30xk: Seryl-tRNA synthetase in complex with a fragment-sized inhibitor ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 30xk
TitleSeryl-tRNA synthetase in complex with a fragment-sized inhibitor (3-cyclopropyl benzoic acid)
ComponentsSerine--tRNA ligase
KeywordsLIGASE / Inhibitor / complex / synthetase / tRNA / fragment / serine
Function / homology
Function and homology information


L-selenocysteine biosynthetic process / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / magnesium ion binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
Serine-tRNA synthetase, type1, N-terminal / Seryl-tRNA synthetase N-terminal domain / Serine-tRNA ligase, type1 / Serine-tRNA ligase catalytic core domain / Serine-tRNA synthetase, type1, N-terminal domain superfamily / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
Similarity search - Domain/homology
: / Serine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsRudusa, L. / Bobrovs, R. / Aleksis, R.
Funding support Latvia, 1items
OrganizationGrant numberCountry
Other government Latvia
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2026
Title: Rapid Fragment Screening by 19F Steady-State Free Precession NMR
Authors: Rudusa, L. / Ozola, S. / Melnykov, K.P. / Filatov, Y.I. / Ryabukhin, S.V. / Bobrovs, R. / Volochnyuk, D.M. / Jaudzems, K. / Aleksis, R.
History
DepositionMay 15, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7323
Polymers48,4781
Non-polymers2542
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint0 kcal/mol
Surface area20660 Å2
Unit cell
Length a, b, c (Å)91.196, 91.196, 127.059
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

-
Components

#1: Protein Serine--tRNA ligase / Seryl-tRNA synthetase / SerRS / Seryl-tRNA(Ser/Sec) synthetase


Mass: 48477.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: serS, b0893, JW0876 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8L1, serine-tRNA ligase
#2: Chemical ChemComp-A1J8R / 3-cyclopropylbenzoic acid


Mass: 162.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 3.15 Å3/Da / Density % sol: 60.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: HEPES pH 7.5 0.1 M, PEG Smear Medium 25% (w/v), Glycerol 20% (w/v)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9406 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 8, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9406 Å / Relative weight: 1
ReflectionResolution: 1.468→49.5 Å / Num. obs: 104619 / % possible obs: 99.9 % / Redundancy: 20.7 % / Biso Wilson estimate: 23.13 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 0
Reflection shellResolution: 1.468→1.493 Å / Num. unique obs: 5080 / CC1/2: 0.359 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→49.5 Å / SU ML: 0.1568 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.243
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.198 5170 4.94 %
Rwork0.1714 99450 -
obs0.1727 104619 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.58 Å2
Refinement stepCycle: LAST / Resolution: 1.47→49.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3221 0 18 152 3391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00473292
X-RAY DIFFRACTIONf_angle_d0.764451
X-RAY DIFFRACTIONf_chiral_restr0.0695498
X-RAY DIFFRACTIONf_plane_restr0.0077589
X-RAY DIFFRACTIONf_dihedral_angle_d16.56871234
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.480.26471560.29153229X-RAY DIFFRACTION98.77
1.48-1.50.30261990.26453258X-RAY DIFFRACTION99.42
1.5-1.520.26581380.25593310X-RAY DIFFRACTION99.68
1.52-1.540.29291690.24753253X-RAY DIFFRACTION99.88
1.54-1.560.2541650.24523293X-RAY DIFFRACTION99.77
1.56-1.580.30861840.24363282X-RAY DIFFRACTION99.94
1.58-1.60.29471330.22243304X-RAY DIFFRACTION100
1.6-1.630.21841870.20613298X-RAY DIFFRACTION100
1.63-1.650.20811780.18823272X-RAY DIFFRACTION100
1.65-1.680.19371450.173310X-RAY DIFFRACTION100
1.68-1.710.20731820.16073286X-RAY DIFFRACTION99.97
1.71-1.740.18911890.15583278X-RAY DIFFRACTION99.97
1.74-1.770.18651590.1453293X-RAY DIFFRACTION100
1.77-1.810.21131820.14463272X-RAY DIFFRACTION99.97
1.81-1.850.16381710.15223318X-RAY DIFFRACTION100
1.85-1.890.16611710.15193302X-RAY DIFFRACTION100
1.89-1.940.1981790.15833284X-RAY DIFFRACTION100
1.94-1.990.18821670.16073334X-RAY DIFFRACTION99.97
1.99-2.050.20471670.14733311X-RAY DIFFRACTION100
2.05-2.120.1741650.14743337X-RAY DIFFRACTION100
2.12-2.190.15481820.15553267X-RAY DIFFRACTION100
2.19-2.280.19961600.16013356X-RAY DIFFRACTION100
2.28-2.380.19831650.173335X-RAY DIFFRACTION100
2.38-2.510.20721720.17893321X-RAY DIFFRACTION100
2.51-2.670.21362110.18873312X-RAY DIFFRACTION100
2.67-2.870.20912040.18523317X-RAY DIFFRACTION100
2.87-3.160.21251710.18333361X-RAY DIFFRACTION100
3.16-3.620.20111690.17763380X-RAY DIFFRACTION100
3.62-4.560.18431690.15153429X-RAY DIFFRACTION100
4.56-49.50.17991810.16913548X-RAY DIFFRACTION99.79

+
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