[English] 日本語
Yorodumi
- PDB-4zib: Crystal Structure of the C-terminal domain of PylRS mutant bound ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zib
TitleCrystal Structure of the C-terminal domain of PylRS mutant bound with 3-benzothienyl-l-alanine and ATP
ComponentsPyrrolysine--tRNA ligase
KeywordsLIGASE / Aminoacyl-tRNA Synthetases / Archaeal Proteins / Evolution / Molecular / Genetic Code / Substrate Specificity
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
3-(1-benzothiophen-3-yl)-L-alanine / ADENOSINE-5'-TRIPHOSPHATE / Pyrrolysine--tRNA ligase
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.054 Å
AuthorsNakamura, A. / Guo, L.T. / Wang, Y.S. / Soll, D.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Probing the active site tryptophan of Staphylococcus aureus thioredoxin with an analog.
Authors: Englert, M. / Nakamura, A. / Wang, Y.S. / Eiler, D. / Soll, D. / Guo, L.T.
History
DepositionApr 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 2.0Oct 14, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.type / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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
Revision 2.1Sep 27, 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
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pyrrolysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,62013
Polymers33,3841
Non-polymers1,23612
Water2,504139
1
A: Pyrrolysine--tRNA ligase
hetero molecules

A: Pyrrolysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,24026
Polymers66,7682
Non-polymers2,47224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area5000 Å2
ΔGint-12 kcal/mol
Surface area23790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.140, 105.140, 70.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

-
Components

-
Protein , 1 types, 1 molecules A

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


Mass: 33384.164 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 185-454) / Mutation: N346G, C348Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88) (archaea)
Strain: ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88
Gene: pylS, MM_1445 / Plasmid: pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 Codon Plus RIL (DE3) / References: UniProt: Q8PWY1, pyrrolysine-tRNAPyl ligase

-
Non-polymers , 5 types, 151 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-4OG / 3-(1-benzothiophen-3-yl)-L-alanine


Type: L-peptide linking / Mass: 221.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11NO2S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 3.39 Å3/Da / Density % sol: 63.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Hepes, MgCl2, PEG3350 / PH range: 7.0-8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.05→42.23 Å / Num. obs: 27798 / % possible obs: 99.4 % / Redundancy: 19.71 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 31.2
Reflection shellResolution: 2.05→2.18 Å / Redundancy: 20.2 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 4.75 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZIM

2zim


Resolution: 2.054→42.233 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 21.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1981 2803 10.08 %
Rwork0.1703 --
obs0.1732 27795 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.054→42.233 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2091 0 77 139 2307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032244
X-RAY DIFFRACTIONf_angle_d0.7723019
X-RAY DIFFRACTIONf_dihedral_angle_d14.096893
X-RAY DIFFRACTIONf_chiral_restr0.028321
X-RAY DIFFRACTIONf_plane_restr0.003400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0536-2.08910.2781450.2331199X-RAY DIFFRACTION98
2.0891-2.1270.24291490.20061265X-RAY DIFFRACTION100
2.127-2.16790.22841280.20171241X-RAY DIFFRACTION100
2.1679-2.21220.26351330.22561261X-RAY DIFFRACTION100
2.2122-2.26030.36871310.31751189X-RAY DIFFRACTION94
2.2603-2.31290.26491190.23561211X-RAY DIFFRACTION96
2.3129-2.37070.25641380.21631246X-RAY DIFFRACTION100
2.3707-2.43480.22911280.20811269X-RAY DIFFRACTION100
2.4348-2.50640.24371350.20571265X-RAY DIFFRACTION100
2.5064-2.58730.25821430.19641244X-RAY DIFFRACTION100
2.5873-2.67980.24471410.20131255X-RAY DIFFRACTION100
2.6798-2.78710.25611350.20231256X-RAY DIFFRACTION100
2.7871-2.91390.22091530.1921231X-RAY DIFFRACTION100
2.9139-3.06750.24231390.1861266X-RAY DIFFRACTION100
3.0675-3.25960.20431470.17061268X-RAY DIFFRACTION100
3.2596-3.51110.20441550.17291238X-RAY DIFFRACTION100
3.5111-3.86430.17271300.1531264X-RAY DIFFRACTION100
3.8643-4.42290.15431530.1321262X-RAY DIFFRACTION100
4.4229-5.57040.16361530.1311263X-RAY DIFFRACTION100
5.5704-42.24150.14671480.14971299X-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