[English] 日本語
Yorodumi
- PDB-4pbs: Crystal structure of the M. jannaschii F9 tRNA synthetase variant... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pbs
TitleCrystal structure of the M. jannaschii F9 tRNA synthetase variant bound to 4-(2-bromoisobutyramido)-phenylalanine (BibaF)
ComponentsTyrosine--tRNA ligase
KeywordsLIGASE / tRNA synthetase / non-natural amino acid
Function / homology
Function and homology information


tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / ATP binding / cytoplasm
Similarity search - Function
Tyrosine-tRNA ligase, type 3 / Tyrosine-tRNA ligase, archaeal/eukaryotic-type / Tyrosine-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / 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. / HUPs ...Tyrosine-tRNA ligase, type 3 / Tyrosine-tRNA ligase, archaeal/eukaryotic-type / Tyrosine-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / 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. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-2L7 / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.011 Å
AuthorsCooley, R.B. / Karplus, P.A. / Mehl, R.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-0448297 United States
CitationJournal: Chembiochem / Year: 2014
Title: Gleaning Unexpected Fruits from Hard-Won Synthetases: Probing Principles of Permissivity in Non-canonical Amino Acid-tRNA Synthetases.
Authors: Cooley, R.B. / Karplus, P.A. / Mehl, R.A.
History
DepositionApr 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 21, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 1.5Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: 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 / refine_hist
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3452
Polymers36,0161
Non-polymers3291
Water3,855214
1
A: Tyrosine--tRNA ligase
hetero molecules

A: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6904
Polymers72,0312
Non-polymers6582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_664-y+1,-x+1,-z-1/21
Buried area2790 Å2
ΔGint-27 kcal/mol
Surface area27680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.470, 101.470, 71.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-518-

HOH

-
Components

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


Mass: 36015.738 Da / Num. of mol.: 1 / Mutation: Y32G, L65E, D158G, I159C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: tyrS, MJ0389 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q57834, tyrosine-tRNA ligase
#2: Chemical ChemComp-2L7 / 4-[(2-bromo-2-methylpropanoyl)amino]-L-phenylalanine


Mass: 329.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17BrN2O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 23% PEG 300, 5% PEG 8000, 10% glycerol and 100 mM Tris
PH range: 7.8-8.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→24.6 Å / Num. obs: 24581 / % possible obs: 94.8 % / Redundancy: 7.8 % / Net I/σ(I): 9.6

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZP1

2zp1


Resolution: 2.011→24.6 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2354 1000 5.05 %Random
Rwork0.1791 ---
obs0.182 19783 77.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.011→24.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2474 0 19 214 2707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062586
X-RAY DIFFRACTIONf_angle_d0.8043484
X-RAY DIFFRACTIONf_dihedral_angle_d15.6311020
X-RAY DIFFRACTIONf_chiral_restr0.043383
X-RAY DIFFRACTIONf_plane_restr0.005450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.011-2.11720.4019190.2981402X-RAY DIFFRACTION12
2.1172-2.24970.2816850.24721704X-RAY DIFFRACTION50
2.2497-2.42330.28471700.23673108X-RAY DIFFRACTION92
2.4233-2.66690.25781740.21543190X-RAY DIFFRACTION93
2.6669-3.05220.24831980.19143250X-RAY DIFFRACTION96
3.0522-3.84310.22921860.15243459X-RAY DIFFRACTION99
3.8431-24.60.19821680.15323670X-RAY DIFFRACTION100
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)
11.83330.65051.6241.56460.87284.4407-0.0611-0.09990.10790.0395-0.05250.0346-0.2280.03290.08860.15620.0011-0.02250.1537-0.00420.177575.645543.2726-4.266
24.6769-0.50461.25954.0361-0.66345.095-0.2292-0.21660.0980.11710.0696-0.2060.00640.01440.14480.2198-0.0339-0.03180.23980.00140.143685.477437.337920.8236
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:195)
2X-RAY DIFFRACTION2(chain A and resid 196:310)

+
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