[English] 日本語
Yorodumi
- PDB-1sry: REFINED CRYSTAL STRUCTURE OF THE SERYL-TRNA SYNTHETASE FROM THERM... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1sry
TitleREFINED CRYSTAL STRUCTURE OF THE SERYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS AT 2.5 ANGSTROMS RESOLUTION
ComponentsSERYL-tRNA SYNTHETASE
KeywordsLIGASE(SYNTHETASE)
Function / homology
Function and homology information


selenocysteine biosynthetic process / seryl-tRNA aminoacylation / serine-tRNA ligase / serine-tRNA ligase activity / serine binding / tRNA binding / protein homodimerization activity / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Serine-tRNA synthetase, tRNA binding domain / 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) / Bira Bifunctional Protein; Domain 2 ...Serine-tRNA synthetase, tRNA binding domain / 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) / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / 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) / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsFujinaga, M. / Berthet-Colominas, C. / Cusack, S.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Refined crystal structure of the seryl-tRNA synthetase from Thermus thermophilus at 2.5 A resolution.
Authors: Fujinaga, M. / Berthet-Colominas, C. / Yaremchuk, A.D. / Tukalo, M.A. / Cusack, S.
#1: Journal: J.Mol.Biol. / Year: 1990
Title: Crystals of Seryl-tRNA Synthetase from Thermus Thermophilus. Preliminary Crystallographic Data
Authors: Garber, M.B. / Yaremchuk, A.D. / Tukalo, M.A. / Egorova, S.P. / Berthet-Colominas, C. / Leberman, R.
#2: Journal: Nature / Year: 1990
Title: Seryl-tRNA Synthetase from Escherichia Coli at 2.5 Angstroms Resolution: A Second Class of Synthetase Structure
Authors: Cusack, S. / Berthet-Colominas, C. / Haetlein, M. / Nassar, N. / Leberman, R.
History
DepositionAug 10, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SERYL-tRNA SYNTHETASE
B: SERYL-tRNA SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)95,7582
Polymers95,7582
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-29 kcal/mol
Surface area36840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.030, 127.460, 63.370
Angle α, β, γ (deg.)90.00, 108.90, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO A 206 / 2: CIS PROLINE - PRO A 245
3: PHE A 262 - GLY A 263 OMEGA =144.25 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: ASP A 265 - VAL A 266 OMEGA =143.24 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: CIS PROLINE - PRO A 385
6: LYS B 60 - ALA B 61 OMEGA =140.39 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
7: CIS PROLINE - PRO B 206 / 8: CIS PROLINE - PRO B 245
9: GLU B 258 - ALA B 259 OMEGA =129.05 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
10: LYS B 264 - ASP B 265 OMEGA =224.46 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
11: VAL B 266 - ARG B 267 OMEGA =210.60 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
12: ARG B 267 - GLY B 268 OMEGA =228.86 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
13: CIS PROLINE - PRO B 385

-
Components

#1: Protein SERYL-tRNA SYNTHETASE


Mass: 47878.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / References: UniProt: P34945, serine-tRNA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.56 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 %satammonium sulfate1drop
350 mMMES1drop
45 mMdithiothreitol1drop
510 mM1dropMgCl2
61 mM1dropNaN3
71 %(v/v)MPD1drop
830-35 %satammonium sulfate1reservoir
98 %MPD1reservoir

-
Data collection

Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 44704 / % possible obs: 97 % / Num. measured all: 234441 / Rmerge(I) obs: 0.06

-
Processing

SoftwareName: GROMOS / Classification: refinement
RefinementResolution: 2.5→10 Å / Rfactor Rwork: 0.184 / σ(F): 0
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6746 0 0 190 6936
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.016
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d0.049
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Software
*PLUS
Name: GROMOS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 10 Å / σ(F): 0 / Rfactor all: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_planar_d0.058
X-RAY DIFFRACTIONo_plane_restr0.05
X-RAY DIFFRACTIONo_chiral_restr0.165

+
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://pdbjlvh1.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