[English] 日本語
Yorodumi
- PDB-6lya: PylRS C-terminus domain mutant bound with 1-Methyl-L-tryptophan a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lya
TitlePylRS C-terminus domain mutant bound with 1-Methyl-L-tryptophan and AMPNP
ComponentsPyrrolysine--tRNA ligase
KeywordsLIGASE / tRNA Synthetase
Function / homology
Function and homology information


pyrrolysine-tRNAPyl ligase / pyrrolysyl-tRNA synthetase activity / tRNA aminoacylation for protein translation / tRNA binding / ATP binding / cytoplasm
Similarity search - Function
Pyrrolysyl-tRNA ligase / Pyrrolysyl-tRNA ligase, N-terminal / Helix hairpin bin / Pyrrolysyl-tRNA ligase, C-terminal / 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. ...Pyrrolysyl-tRNA ligase / Pyrrolysyl-tRNA ligase, N-terminal / Helix hairpin bin / Pyrrolysyl-tRNA ligase, C-terminal / 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) / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / 1-Methyl-L-tryptophan / Pyrrolysine--tRNA ligase / Pyrrolysine--tRNA ligase
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59070211581 Å
AuthorsWeng, J.H. / Tsai, M.D. / Wang, Y.S.
Funding support Taiwan, 3items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-KPQ-109-TPP2 Taiwan
Academia Sinica (Taiwan)AS-KPQ-105-TPP Taiwan
Ministry of Science and Technology (MoST, Taiwan)107-2113-M-001-025-MY3 Taiwan
CitationJournal: Biochemistry / Year: 2020
Title: Probing the Active Site of Deubiquitinase USP30 with Noncanonical Tryptophan Analogues.
Authors: Jiang, H.K. / Wang, Y.H. / Weng, J.H. / Kurkute, P. / Li, C.L. / Lee, M.N. / Chen, P.J. / Tseng, H.W. / Tsai, M.D. / Wang, Y.S.
History
DepositionFeb 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Derived calculations / Structure summary
Category: audit_author / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.2Jan 27, 2021Group: Derived calculations / Structure summary / Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pyrrolysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9598
Polymers32,0001
Non-polymers9597
Water4,414245
1
A: Pyrrolysine--tRNA ligase
hetero molecules

A: Pyrrolysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,91816
Polymers63,9992
Non-polymers1,91914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_685-x+1,-y+3,z1
Buried area8490 Å2
ΔGint-35 kcal/mol
Surface area22680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.450, 105.450, 71.824
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Space group name HallP64
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Pyrrolysine--tRNA ligase / Pyrrolysyl-tRNA synthetase / PylRS


Mass: 31999.602 Da / Num. of mol.: 1 / Fragment: C-terminus domain / Mutation: N346G,C348Q,V401G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Gene: pylS, DU43_20175, DU67_18120 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0F8JXW8, UniProt: Q8PWY1*PLUS, pyrrolysine-tRNAPyl ligase

-
Non-polymers , 5 types, 252 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EXL / 1-Methyl-L-tryptophan / (2S)-2-azanyl-3-(1-methylindol-3-yl)propanoic acid


Type: L-peptide linking / Mass: 218.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.83 Å3/Da / Density % sol: 67.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM HEPES, 10% PEG 8000, 10% Ethylene Glycerol

-
Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.59→45.68 Å / Num. obs: 60796 / % possible obs: 99.75 % / Redundancy: 8.7 % / Biso Wilson estimate: 29.2378296719 Å2 / Rpim(I) all: 0.025 / Rrim(I) all: 0.073 / Net I/σ(I): 15.5
Reflection shellResolution: 1.59→1.65 Å / Num. unique obs: 5945 / Rpim(I) all: 0.41 / Rrim(I) all: 1.232

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Blu-Icedata collection
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZCE

2zce


Resolution: 1.59070211581→42.5024408741 Å / SU ML: 0.183837184895 / Cross valid method: FREE R-VALUE / σ(F): 1.35019049263 / Phase error: 21.2665780124
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.194185300191 2951 4.85393775906 %
Rwork0.178010944003 57845 -
obs0.178800562783 60796 99.7031667678 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.6262790885 Å2
Refinement stepCycle: LAST / Resolution: 1.59070211581→42.5024408741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2117 0 61 245 2423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01259660453552235
X-RAY DIFFRACTIONf_angle_d1.191719728123009
X-RAY DIFFRACTIONf_chiral_restr0.0778544122735321
X-RAY DIFFRACTIONf_plane_restr0.00738830904116386
X-RAY DIFFRACTIONf_dihedral_angle_d21.8048867188867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.590703-1.61680.2856998260931350.2914764291392615X-RAY DIFFRACTION95.3867499133
1.6168-1.64470.263424618541400.2679972262622730X-RAY DIFFRACTION99.9651689307
1.6447-1.67460.2776637146761440.2516843355152774X-RAY DIFFRACTION100
1.6746-1.70680.2673962845941460.2653687705712724X-RAY DIFFRACTION99.930362117
1.7068-1.74160.2869278067841500.2456806334082729X-RAY DIFFRACTION99.7920277296
1.7416-1.77950.2204453593421250.2441678703712763X-RAY DIFFRACTION99.8616874136
1.7795-1.82090.2851419768721430.2509893111012765X-RAY DIFFRACTION99.8969426314
1.8209-1.86640.2573374253211270.2355318452372740X-RAY DIFFRACTION100
1.8664-1.91690.2183016442871410.2243816996672785X-RAY DIFFRACTION100
1.9169-1.97330.2150229729281610.2058158100522723X-RAY DIFFRACTION99.7923875433
1.9733-2.0370.2328736871841490.2021758193722730X-RAY DIFFRACTION100
2.037-2.10980.2346378827891080.2037834368692800X-RAY DIFFRACTION99.9656239257
2.1098-2.19420.2098903103391300.1889415496922765X-RAY DIFFRACTION99.9309630652
2.1942-2.29410.199269035571420.1908188766532735X-RAY DIFFRACTION99.8611593197
2.2941-2.4150.2065051237661400.1883109137252788X-RAY DIFFRACTION100
2.415-2.56630.2161294944151380.1883971243542758X-RAY DIFFRACTION99.89651604
2.5663-2.76450.2051558463951460.1819485832272775X-RAY DIFFRACTION99.7950119576
2.7645-3.04260.1890041446661450.1751289445782754X-RAY DIFFRACTION99.9655172414
3.0426-3.48270.1471736933311390.1586769425812769X-RAY DIFFRACTION99.8283556471
3.4827-4.38710.1488778434321460.1462719271172794X-RAY DIFFRACTION99.8302207131
4.3871-42.5020.2033119836251560.1584811338062829X-RAY DIFFRACTION100

+
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