[English] 日本語
Yorodumi
- PDB-4s02: Biphenylalanine modified threonyl-tRNA synthetase from Pyrococcus... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4s02
TitleBiphenylalanine modified threonyl-tRNA synthetase from Pyrococcus abyssi: I11BIF, F42W, Y79A, and F123Y mutant
ComponentsThreonine--tRNA ligase
KeywordsLIGASE / beta-alpha-beta fold / editing domain / tRNA-synthetase / Biphenylalanine and unnatural amino acid / threonine-tRNA ligase
Function / homology
Function and homology information


threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA binding / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
Threonyl-tRNA synthetase, editing domain, archaea / Archaea-specific editing domain of threonyl-tRNA synthetase / D-tyrosyl-tRNA(Tyr) deacylase / D-aminoacyl-tRNA deacylase-like superfamily / Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / : / D-tyrosyl-trna(Tyr) Deacylase; Chain: A; / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) ...Threonyl-tRNA synthetase, editing domain, archaea / Archaea-specific editing domain of threonyl-tRNA synthetase / D-tyrosyl-tRNA(Tyr) deacylase / D-aminoacyl-tRNA deacylase-like superfamily / Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / : / D-tyrosyl-trna(Tyr) Deacylase; Chain: A; / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / 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) / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Threonine--tRNA ligase
Similarity search - Component
Biological speciesPyrococcus abyssi GE5 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPearson, A.D. / Mills, J.H. / Song, Y. / Nasertorabi, F. / Han, G.W. / Baker, D. / Stevens, R.C. / Schultz, P.G.
CitationJournal: Science / Year: 2015
Title: Transition states. Trapping a transition state in a computationally designed protein bottle.
Authors: Pearson, A.D. / Mills, J.H. / Song, Y. / Nasertorabi, F. / Han, G.W. / Baker, D. / Stevens, R.C. / Schultz, P.G.
History
DepositionDec 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Sep 20, 2023Group: 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Threonine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7514
Polymers17,4331
Non-polymers3183
Water1,24369
1
A: Threonine--tRNA ligase
hetero molecules

A: Threonine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5038
Polymers34,8662
Non-polymers6376
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_585-x,-y+3,z1
Unit cell
Length a, b, c (Å)52.715, 77.284, 93.153
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-303-

HOH

-
Components

#1: Protein Threonine--tRNA ligase / Threonyl-tRNA synthetase / ThrRS


Mass: 17433.014 Da / Num. of mol.: 1 / Fragment: threonyl-tRNA synthetase / Mutation: I11BIF, F42W, Y79A, F123Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / Gene: PAB1490, PYRAB13430, thrS / Plasmid: pET-22b and pULTRA / Production host: Escherichia coli (E. coli) / Strain (production host): bl21(de3) / References: UniProt: Q9UZ14, threonine-tRNA ligase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M sodium citrate, 15% PEG 6000, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 1, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 14118 / % possible obs: 99.5 % / Redundancy: 11 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 16.6
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 8.1 / Num. unique all: 2030 / % possible all: 100

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.8.0049refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1y2q
Resolution: 1.95→24.1 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.245 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19595 709 5 %RANDOM
Rwork0.16333 ---
obs0.1649 13408 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.616 Å2
Baniso -1Baniso -2Baniso -3
1--13.7 Å2-0 Å2-0 Å2
2--2.9 Å20 Å2
3---10.8 Å2
Refinement stepCycle: LAST / Resolution: 1.95→24.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1101 0 21 69 1191
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191201
X-RAY DIFFRACTIONr_bond_other_d0.0020.021186
X-RAY DIFFRACTIONr_angle_refined_deg1.7972.0011622
X-RAY DIFFRACTIONr_angle_other_deg0.83632739
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9765148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93324.31451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.19115216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.705158
X-RAY DIFFRACTIONr_chiral_restr0.1050.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211336
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02256
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2682.248580
X-RAY DIFFRACTIONr_mcbond_other2.2542.242579
X-RAY DIFFRACTIONr_mcangle_it3.2163.341732
X-RAY DIFFRACTIONr_mcangle_other3.2153.347733
X-RAY DIFFRACTIONr_scbond_it3.9792.935621
X-RAY DIFFRACTIONr_scbond_other3.9722.936621
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1024.149891
X-RAY DIFFRACTIONr_long_range_B_refined8.70120.3291346
X-RAY DIFFRACTIONr_long_range_B_other8.70320.3491347
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 58 -
Rwork0.158 973 -
obs--99.81 %
Refinement TLS params.Method: refined / Origin x: 1.9835 Å / Origin y: 104.3249 Å / Origin z: 19.2131 Å
111213212223313233
T0.0116 Å20.0158 Å2-0.0021 Å2-0.0592 Å2-0.0092 Å2--0.0177 Å2
L1.5311 °2-0.4788 °2-0.0108 °2-1.187 °2-0.5723 °2--0.7427 °2
S-0.0839 Å °-0.078 Å °-0.0664 Å °0.083 Å °-0.017 Å °-0.0407 Å °-0.0346 Å °-0.0333 Å °0.1009 Å °

+
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