[English] 日本語
Yorodumi
- PDB-8i2m: The crystal structure of homodimeric E. coli tryptophanyl-tRNA sy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8i2m
TitleThe crystal structure of homodimeric E. coli tryptophanyl-tRNA synthetase bound with niraparib at one of its two active sites
ComponentsTryptophan--tRNA ligase
KeywordsLIGASE / tryptophanyl-tRNA synthetase / fragment screening / antibacterials
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
Chem-3JD / TRYPTOPHANYL-5'AMP / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsXiang, M. / Zhou, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22177140 China
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: An asymmetric structure of bacterial TrpRS supports the half-of-the-sites catalytic mechanism and facilitates antimicrobial screening.
Authors: Xiang, M. / Xia, K. / Chen, B. / Luo, Z. / Yu, Y. / Jiang, L. / Zhou, H.
History
DepositionJan 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
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)77,8897
Polymers76,7472
Non-polymers1,1425
Water6,287349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-73 kcal/mol
Surface area26760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.656, 79.761, 77.338
Angle α, β, γ (deg.)90.00, 106.32, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 38373.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: trpS, b3384, JW3347 / Production host: Escherichia coli (E. coli) / References: UniProt: P00954, tryptophan-tRNA ligase
#2: Chemical ChemComp-3JD / 2-{4-[(3S)-piperidin-3-yl]phenyl}-2H-indazole-7-carboxamide / Niraparib


Mass: 320.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N4O / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, anticancer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.16M Ammonium sulfate, 0.1M HEPES pH 7.5, 25% PEG 3350

-
Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Mar 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 42029 / % possible obs: 99.9 % / Redundancy: 5 % / CC1/2: 0.994 / Rpim(I) all: 0.052 / Rrim(I) all: 0.121 / Net I/σ(I): 11.1
Reflection shellResolution: 2.1→2.21 Å / % possible obs: 100 % / Redundancy: 3.2 % / Num. measured all: 19573 / Num. unique obs: 6115 / CC1/2: 0.766 / Rpim(I) all: 0.31 / Rrim(I) all: 0.57 / Net I/σ(I) obs: 2.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
SCALAdata scaling
MOLREPphasing
CrysalisProdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V0I

5v0i


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.91 / SU B: 5.183 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23439 2095 5 %RANDOM
Rwork0.2015 ---
obs0.20313 39904 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.242 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å20.24 Å2
2--1.36 Å20 Å2
3----0.57 Å2
Refinement stepCycle: 1 / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5046 0 76 349 5471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195225
X-RAY DIFFRACTIONr_bond_other_d0.0010.024749
X-RAY DIFFRACTIONr_angle_refined_deg1.1351.9677095
X-RAY DIFFRACTIONr_angle_other_deg0.875311002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2545652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.92824.784232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.56115853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4311525
X-RAY DIFFRACTIONr_chiral_restr0.0590.2797
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215872
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021025
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5492.0752622
X-RAY DIFFRACTIONr_mcbond_other0.5472.0752619
X-RAY DIFFRACTIONr_mcangle_it0.9953.1083269
X-RAY DIFFRACTIONr_mcangle_other0.9943.1093269
X-RAY DIFFRACTIONr_scbond_it0.4812.1072603
X-RAY DIFFRACTIONr_scbond_other0.4782.0982591
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8453.1253809
X-RAY DIFFRACTIONr_long_range_B_refined2.32424.7935977
X-RAY DIFFRACTIONr_long_range_B_other2.1924.6365897
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 154 -
Rwork0.255 2928 -
obs--99.97 %

+
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