[English] 日本語
Yorodumi
- PDB-7ap3: Crystal structure of E. coli tyrosyl-tRNA synthetase in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ap3
TitleCrystal structure of E. coli tyrosyl-tRNA synthetase in complex with TyrS7HMDDA
ComponentsTyrosine--tRNA ligase
KeywordsLIGASE / protein-inhibitor complex / tRNA aminoacylation
Function / homology
Function and homology information


tRNA aminoacylation / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / protein homodimerization activity / RNA binding / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
Tyrosine-tRNA ligase, bacterial-type, type 1 / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-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 / S4 RNA-binding domain / RNA-binding S4 domain ...Tyrosine-tRNA ligase, bacterial-type, type 1 / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-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 / S4 RNA-binding domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / S4 domain / S4 RNA-binding domain profile.
Similarity search - Domain/homology
Chem-RRB / Tyrosine--tRNA ligase / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDe Graef, S. / Pang, L. / Strelkov, S.V. / Weeks, S.D.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)1S53518N Belgium
CitationJournal: Molecules / Year: 2020
Title: Synthesis and Biological Evaluation of 1,3-Dideazapurine-Like 7-Amino-5-Hydroxymethyl-Benzimidazole Ribonucleoside Analogues as Aminoacyl-tRNA Synthetase Inhibitors.
Authors: Zhang, B. / Pang, L. / Nautiyal, M. / De Graef, S. / Gadakh, B. / Lescrinier, E. / Rozenski, J. / Strelkov, S.V. / Weeks, S.D. / Van Aerschot, A.
History
DepositionOct 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)96,3116
Polymers95,1902
Non-polymers1,1214
Water8,665481
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-46 kcal/mol
Surface area35800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.166, 65.124, 90.978
Angle α, β, γ (deg.)90.000, 101.330, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Tyrosine--tRNA ligase / Tyrosyl-tRNA synthetase / TyrRS


Mass: 47594.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Strain: DE3 / Gene: tyrS, ECBD_2006 / Plasmid: pETRUK / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: A0A140NBN7, UniProt: P0AGJ9*PLUS, tyrosine-tRNA ligase
#2: Chemical ChemComp-RRB / [(2~{R},3~{S},4~{R},5~{R})-5-[7-azanyl-5-(hydroxymethyl)benzimidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-(4-hydroxyphenyl)propanoyl]sulfamate


Mass: 537.543 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H27N5O9S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 481 / 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: 2.51 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: Holo enzyme crystals were grown in 0.1 M BIS-TRIS pH 6.5, 10-15% PEG 3350, 20 mM glutamate pH 6 (1M stock solution adjusted to pH 5) and 20% (v/v) ethylene glycol. For soaking crystals were ...Details: Holo enzyme crystals were grown in 0.1 M BIS-TRIS pH 6.5, 10-15% PEG 3350, 20 mM glutamate pH 6 (1M stock solution adjusted to pH 5) and 20% (v/v) ethylene glycol. For soaking crystals were transferred to a drop containing mother liquor supplemented with 2 mM inhibitor.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.968625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968625 Å / Relative weight: 1
ReflectionResolution: 1.998→65.12 Å / Num. obs: 63743 / % possible obs: 99.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 29.52 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.065 / Rrim(I) all: 0.126 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.5 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.110.9063275992660.7110.5571.0671.499.5
6.32-65.120.035739121220.9990.0210.04122.499.4

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimless0.6.2data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OUD

4oud


Resolution: 2→54.681 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2533 2467 3.88 %
Rwork0.2028 61154 -
obs0.2048 63621 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.77 Å2 / Biso mean: 41.4637 Å2 / Biso min: 16.55 Å2
Refinement stepCycle: final / Resolution: 2→54.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6428 0 76 481 6985
Biso mean--30.72 41.2 -
Num. residues----826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076635
X-RAY DIFFRACTIONf_angle_d0.8448988
X-RAY DIFFRACTIONf_chiral_restr0.048985
X-RAY DIFFRACTIONf_plane_restr0.0051219
X-RAY DIFFRACTIONf_dihedral_angle_d7.23958
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.03630.32011510.3086339599
2.0363-2.07790.36131180.2952335199
2.0779-2.12310.33691460.28336799
2.1231-2.17250.32981380.2677339999
2.1725-2.22680.28581370.2464338199
2.2268-2.2870.31351410.2493335899
2.287-2.35430.28621270.2389339099
2.3543-2.43030.28581320.22793405100
2.4303-2.51720.29721350.22293392100
2.5172-2.61790.28141430.2119339299
2.6179-2.73710.321520.2108338499
2.7371-2.88140.27311260.2112337999
2.8814-3.06190.25431450.208340699
3.0619-3.29830.221340.2001339699
3.2983-3.63010.22421380.1899342799
3.6301-4.15530.20171170.165341999
4.1553-5.23460.19261570.1605338198
5.2346-54.6810.25661300.1795353299
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)
11.3807-0.21591.41261.1021-0.44582.3963-0.0507-0.22310.02960.11320.00410.0027-0.1087-0.20620.03080.22690.0119-0.01070.322-0.0170.1884-39.04062.1689-9.5796
22.7052-1.7219-1.83283.64151.6633.01420.0059-0.09430.11390.1933-0.0049-0.3119-0.19150.28530.01310.3389-0.0499-0.08990.36410.03610.2369-17.20467.57257.9976
32.7571.7023-0.34861.0565-0.23240.07010.28230.0263-0.0589-1.0389-0.0304-1.883-0.08420.44170.0740.468-0.00830.49250.73410.00531.44839.31194.6147-3.2653
42.00280.21110.57850.9365-0.00041.9513-0.02360.17170.0368-0.06250.0310.0167-0.02140.0432-0.00920.19460.0022-0.02870.20990.0070.2279-48.75140.9213-45.1946
52.83671.53520.07860.9403-0.21290.6741-0.09340.36080.6821-0.01430.09820.3018-0.0956-0.14850.00220.22570.0187-0.04650.31750.040.3351-64.03457.9659-54.2067
63.4119-0.1449-0.22370.4853-0.00060.68620.04030.41820.1019-0.0013-0.0616-0.0264-0.04330.1708-0.0090.2072-0.0166-0.03180.29870.0490.2057-86.95294.8879-58.2371
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 235 )A5 - 235
2X-RAY DIFFRACTION2chain 'A' and (resid 243 through 329 )A243 - 329
3X-RAY DIFFRACTION3chain 'A' and (resid 330 through 424 )A330 - 424
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 216 )B5 - 216
5X-RAY DIFFRACTION5chain 'B' and (resid 217 through 267 )B217 - 267
6X-RAY DIFFRACTION6chain 'B' and (resid 268 through 424 )B268 - 424

+
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