[English] 日本語
Yorodumi
- PDB-1mau: Crystal structure of Tryptophanyl-tRNA Synthetase Complexed with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mau
TitleCrystal structure of Tryptophanyl-tRNA Synthetase Complexed with ATP and Tryptophanamide in a Pre-Transition state Conformation
Componentstryptophan-tRNA ligase
KeywordsLIGASE / Amino-acyl tRNA synthetase / Rossmann fold / atp binding site / pre-transition state
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophanyl-tRNA aminoacylation / tryptophan-tRNA ligase activity / ATP binding / cytoplasm
Similarity search - Function
Tryptophan-tRNA ligase, bacterial-type / : / Tryptophan-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 ...Tryptophan-tRNA ligase, bacterial-type / : / Tryptophan-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
ADENOSINE-5'-TRIPHOSPHATE / CITRIC ACID / L-TRYPTOPHANAMIDE / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SIR / Resolution: 2.15 Å
AuthorsRetailleau, P. / Huang, X. / Yin, Y. / Hu, M. / Weinreb, V. / Vachette, P. / Vonrhein, C. / Bricogne, G. / Roversi, P. / Ilyin, V. / Carter Jr., C.W.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Interconversion of ATP binding and conformational free energies by tryptophanyl-tRNA synthetase: structures of ATP bound to open and closed, pre-transition-state conformations.
Authors: Retailleau, P. / Huang, X. / Yin, Y. / Hu, M. / Weinreb, V. / Vachette, P. / Vonrhein, C. / Bricogne, G. / Roversi, P. / Ilyin, V. / Carter, C.W.
History
DepositionAug 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: tryptophan-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4529
Polymers37,2261
Non-polymers1,2268
Water2,144119
1
A: tryptophan-tRNA ligase
hetero molecules

A: tryptophan-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,90418
Polymers74,4512
Non-polymers2,45216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area9150 Å2
ΔGint-69 kcal/mol
Surface area26170 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.133, 62.133, 217.807
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein tryptophan-tRNA ligase / Tryptophanyl-tRNA Synthetase


Mass: 37225.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P00953, tryptophan-tRNA ligase

-
Non-polymers , 7 types, 127 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-LTN / L-TRYPTOPHANAMIDE


Mass: 203.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13N3O
#6: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.42 %
Crystal growTemperature: 310 K / Method: microdialysis / pH: 7.5
Details: sodium citrate, magnesium chloride, sodium ATP , l-tryptophanamide, pH 7.5, MICRODIALYSIS, temperature 310K
Crystal grow
*PLUS
Temperature: 35 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 mg/mlprotein11
20.6 Mpotassium phosphate11
350 %(v/v)glycerol11
41 Msodium citrate12
510 mMATP12
610 mM12MgCl2
750000 mMtryptophanamide12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. all: 25809 / Num. obs: 23318 / % possible obs: 90.5 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 35.5 Å2 / Rsym value: 0.079 / Net I/σ(I): 16
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.75 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 1933 / Rsym value: 0.32 / % possible all: 77.5
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 335452 / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
% possible obs: 77.5 % / Rmerge(I) obs: 0.32

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
BUSTER-TNTrefinement
RefinementMethod to determine structure: SIR
Starting model: PDB ENTRY 1M83

1m83


Resolution: 2.15→20 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2254 10 %random
Rwork0.208 ---
all0.212 24050 --
obs0.212 22227 --
Refinement stepCycle: LAST / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2605 0 79 119 2803
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00627452
X-RAY DIFFRACTIONt_angle_deg0.97436982
X-RAY DIFFRACTIONt_dihedral_angle_d17.04816110
X-RAY DIFFRACTIONt_trig_c_planes0.009902
X-RAY DIFFRACTIONt_gen_planes0.0154535
X-RAY DIFFRACTIONt_it1.363274620
X-RAY DIFFRACTIONt_nbd1.1761305
X-RAY DIFFRACTIONt_incorr_chiral_ct0
Refinement
*PLUS
Num. reflection obs: 19973 / % reflection Rfree: 10 % / Rfactor Rfree: 0.244 / Rfactor Rwork: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_angle_deg0.975
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.0480

+
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