[English] 日本語
Yorodumi
- PDB-2du7: Crystal structure of Methanococcus jannacshii O-phosphoseryl-tRNA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2du7
TitleCrystal structure of Methanococcus jannacshii O-phosphoseryl-tRNA synthetase
ComponentsO-phosphoseryl-tRNA synthetase
KeywordsLIGASE / alpha4 tetramer / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


O-phospho-L-serine-tRNA ligase / phosphoserine-tRNA(Cys) ligase activity / phenylalanyl-tRNA aminoacylation / phenylalanine-tRNA ligase activity / tRNA binding / ATP binding / cytoplasm
Similarity search - Function
O-phosphoseryl-tRNA(Cys) ligase / O-phosphoserine--tRNA(Cys) ligase, C-terminal domain / O-phosphoseryl-tRNA synthetase C-terminal domain / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / 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) ...O-phosphoseryl-tRNA(Cys) ligase / O-phosphoserine--tRNA(Cys) ligase, C-terminal domain / O-phosphoseryl-tRNA synthetase C-terminal domain / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / 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) / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
O-phosphoserine--tRNA(Cys) ligase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsFukunaga, R. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea.
Authors: Fukunaga, R. / Yokoyama, S.
History
DepositionJul 20, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: O-phosphoseryl-tRNA synthetase
B: O-phosphoseryl-tRNA synthetase
C: O-phosphoseryl-tRNA synthetase
D: O-phosphoseryl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)254,1104
Polymers254,1104
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26990 Å2
ΔGint-161 kcal/mol
Surface area116630 Å2
MethodPISA, PQS
2
A: O-phosphoseryl-tRNA synthetase
B: O-phosphoseryl-tRNA synthetase
C: O-phosphoseryl-tRNA synthetase
D: O-phosphoseryl-tRNA synthetase

A: O-phosphoseryl-tRNA synthetase
B: O-phosphoseryl-tRNA synthetase
C: O-phosphoseryl-tRNA synthetase
D: O-phosphoseryl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)508,2218
Polymers508,2218
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area63650 Å2
ΔGint-375 kcal/mol
Surface area223580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.354, 299.455, 125.877
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein
O-phosphoseryl-tRNA synthetase / Putative phenylalanyl-tRNA synthetase alpha chain-like protein MJ1660


Mass: 63527.578 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: pET26b / Production host: Escherichia coli (E. coli)
References: UniProt: Q59054, Ligases; Forming carbon-oxygen bonds; Ligases forming aminoacyl-tRNA and related compounds

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 11.25% PEG 4000, 75mM Na-citrate, 75mM ADA-NaOH buffer (pH 6.7), VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→20 Å / Num. all: 43084 / Num. obs: 42030 / % possible obs: 97.6 % / Observed criterion σ(I): 0
Reflection shellResolution: 3.6→3.73 Å / % possible all: 94.1

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DU3

2du3


Resolution: 3.6→19.79 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 7089748.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.387 4236 10.1 %RANDOM
Rwork0.33 ---
obs0.33 42030 97.5 %-
all-43084 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.9985 Å2 / ksol: 0.194656 e/Å3
Displacement parametersBiso mean: 129.2 Å2
Baniso -1Baniso -2Baniso -3
1-12.16 Å20 Å20 Å2
2---3.37 Å20 Å2
3----8.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.67 Å0.53 Å
Luzzati d res low-5 Å
Luzzati sigma a1 Å0.81 Å
Refinement stepCycle: LAST / Resolution: 3.6→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17516 0 0 0 17516
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it23.171.5
X-RAY DIFFRACTIONc_mcangle_it35.92
X-RAY DIFFRACTIONc_scbond_it28.242
X-RAY DIFFRACTIONc_scangle_it41.272.5
LS refinement shellResolution: 3.6→3.82 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.429 669 10 %
Rwork0.373 6045 -
obs--94.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4dna-rna_rep.paramdna-rna_rep.top

+
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