[English] 日本語
Yorodumi
- PDB-1asz: THE ACTIVE SITE OF YEAST ASPARTYL-TRNA SYNTHETASE: STRUCTURAL AND... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 1asz
TitleTHE ACTIVE SITE OF YEAST ASPARTYL-TRNA SYNTHETASE: STRUCTURAL AND FUNCTIONAL ASPECTS OF THE AMINOACYLATION REACTION
Components
  • ASPARTYL-tRNA SYNTHETASE
  • T-RNA (75-MER)
KeywordsCOMPLEX (AMINOACYL-TRNA SYNTHASE/TRNA) / COMPLEX (AMINOACYL-TRNA SYNTHASE-TRNA) / COMPLEX (AMINOACYL-TRNA SYNTHASE-TRNA) complex
Function / homologyAspartyl/Asparaginyl-tRNA synthetase, class IIb / Aminoacyl-tRNA synthetase, class II (D/K/N) / Aminoacyl-transfer RNA synthetases class-II family profile. / OB-fold nucleic acid binding domain / tRNA synthetases class II (D, K and N) / Nucleic acid-binding, OB-fold / Aminoacyl-tRNA synthetase, class II / Aspartate-tRNA synthetase, type 2 / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / aspartate-tRNA ligase ...Aspartyl/Asparaginyl-tRNA synthetase, class IIb / Aminoacyl-tRNA synthetase, class II (D/K/N) / Aminoacyl-transfer RNA synthetases class-II family profile. / OB-fold nucleic acid binding domain / tRNA synthetases class II (D, K and N) / Nucleic acid-binding, OB-fold / Aminoacyl-tRNA synthetase, class II / Aspartate-tRNA synthetase, type 2 / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / aspartate-tRNA ligase / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / aminoacyl-tRNA synthetase multienzyme complex / RNA binding / ATP binding / nucleus / cytosol / cytoplasm / Aspartate--tRNA ligase, cytoplasmic
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodX-RAY DIFFRACTION / 3 Å resolution
AuthorsCavarelli, J. / Rees, B. / Thierry, J.C. / Moras, D.
Citation
Journal: EMBO J. / Year: 1994
Title: The active site of yeast aspartyl-tRNA synthetase: structural and functional aspects of the aminoacylation reaction.
Authors: Cavarelli, J. / Eriani, G. / Rees, B. / Ruff, M. / Boeglin, M. / Mitschler, A. / Martin, F. / Gangloff, J. / Thierry, J.C. / Moras, D.
#1: Journal: Biochimie / Year: 1993
Title: Yeast Aspartyl-tRNA Synthetase: A Structural View of the Aminoacylation Reaction Aminoacyl-tRNA Synthetase
Authors: Cavarelli, J. / Rees, B. / Thierry, J.C. / Moras, D.
#2: Journal: Nature / Year: 1993
Title: Yeast tRNA Asp Recognition by its Cognate Class II Aminoacyl-tRNA Synthetase
Authors: Cavarelli, J. / Rees, B. / Ruff, M. / Thierry, J.C. / Moras, D.
#3: Journal: Science / Year: 1991
Title: Class II Aminoacyl Transfer RNA Synthetases: Crystal Structure of Yeast Aspartyl-tRNA Synthetase Complexed with tRNA Asp
Authors: Ruff, M. / Krishnaswamy, S. / Boeglin, M. / Poterszman, A. / Mitschler, A. / Podjarny, A. / Rees, B. / Thierry, J.C. / Moras, D.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 19, 1995 / Release: May 8, 1995
RevisionDateData content typeGroupProviderType
1.0May 8, 1995Structure modelrepositoryInitial release
1.1May 22, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
R: T-RNA (75-MER)
S: T-RNA (75-MER)
A: ASPARTYL-tRNA SYNTHETASE
B: ASPARTYL-tRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,4316
Polyers160,4164
Non-polymers1,0142
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)211.270, 145.350, 86.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP 21 21 2
Atom site foot note1: CIS PROLINE - PRO A 557 / 2: CIS PROLINE - PRO B 557
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 68 .. R 676 B 68 .. S 676 0.91

-
Components

#1: RNA chain T-RNA (75-MER)


Mass: 24181.369 Da / Num. of mol.: 2 / References: aspartate-tRNA ligase
#2: Protein/peptide ASPARTYL-tRNA SYNTHETASE


Mass: 56026.750 Da / Num. of mol.: 2
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
References: UniProt: P04802
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.12 / Density percent sol: 70.18 %
Crystal
*PLUS
Density percent sol: 69 %
Crystal grow
*PLUS
Temp: 4 ℃ / Method: vapor diffusion, hanging drop / pH: 7.5
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
140 mMTris-maleate/NaOH1drop
25 mM1dropMgCl2
325 %(w/v)ammonium sulfate1drop
410 mg/mlaspartyl-tRNA synthetase1drop
560 %(w/v)ammonium sulfate1reservoir
64.8 mg/mltRNAAsp1drop

-
Data collection

DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Collection date: Jan 1, 1992
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNumber obs: 46698 / Observed criterion sigma I: 1 / Rmerge I obs: 0.088 / Redundancy: 2.9 % / Percent possible obs: 87
Reflection
*PLUS
D resolution high: 3 Å / Number measured all: 135407

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
MARXDSdata reduction
X-PLORphasing
RefineDetails: TRNA RIBOSES 607, 609, 617, 618, 619, 637, 648, 658, 660, 676, FROM EACH CHAIN, HAVE BEEN CONSTRAINED TO 2' ENDO PUCKER. ALL OTHER TRNA RIBOSES ARE 3' ENDO PUCKER.
Sigma F: 3
Displacement parametersB iso mean: 3 Å2
Least-squares processR factor R work: 0.203 / R factor obs: 0.203 / Highest resolution: 3 Å / Lowest resolution: 7 Å / Number reflection obs: 42994 / Percent reflection obs: 8
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refine hist #LASTHighest resolution: 3 Å / Lowest resolution: 7 Å
Number of atoms included #LASTProtein: 7892 / Nucleic acid: 3204 / Ligand: 62 / Solvent: 0 / Total: 11158
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at EBI / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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