[English] 日本語
Yorodumi
- PDB-6aap: Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6aap
TitleCrystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) complexed with ZaeSeCys
ComponentsPyrrolysine--tRNA ligase
KeywordsTRANSLATION / aminoacyl-tRNA synthetase / non-natural amino acids
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
Chem-9U6 / ADENOSINE-5'-TRIPHOSPHATE / Pyrrolysine--tRNA ligase
Similarity search - Component
Biological speciesMethanosarcina mazei JCM 9314 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsYanagisawa, T. / Kuratani, M. / Yokoyama, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)24550203 Japan
CitationJournal: Cell Chem Biol / Year: 2019
Title: Structural Basis for Genetic-Code Expansion with Bulky Lysine Derivatives by an Engineered Pyrrolysyl-tRNA Synthetase.
Authors: Yanagisawa, T. / Kuratani, M. / Seki, E. / Hino, N. / Sakamoto, K. / Yokoyama, S.
History
DepositionJul 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author / entity_src_gen
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
Revision 1.2Aug 7, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Nov 22, 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 / pdbx_struct_conn_angle / struct_conn
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.ptnr2_symmetry / _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_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pyrrolysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2726
Polymers31,3471
Non-polymers9255
Water4,918273
1
A: Pyrrolysine--tRNA ligase
hetero molecules

A: Pyrrolysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,54512
Polymers62,6942
Non-polymers1,85110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6850 Å2
ΔGint-73 kcal/mol
Surface area22490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.797, 43.609, 72.478
Angle α, β, γ (deg.)90.00, 119.67, 90.00
Int Tables number5
Space group name H-MC121

-
Components

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


Mass: 31346.982 Da / Num. of mol.: 1 / Mutation: Y306A, Y384F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei JCM 9314 (archaea)
Gene: pylS / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): rosetta / References: UniProt: Q8PWY1, pyrrolysine-tRNAPyl ligase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: 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
#4: Chemical ChemComp-9U6 / 3-[(2-{[(benzyloxy)carbonyl]amino}ethyl)selanyl]-L-alanine


Type: peptide linking / Mass: 345.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H18N2O4Se
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe sequence reference Q8PWY1 (PYLS_METMA) is derived from a different strain (Methanosarcina mazei ...The sequence reference Q8PWY1 (PYLS_METMA) is derived from a different strain (Methanosarcina mazei Go1, TaxID 192952). Residue E444G is a natural mutation observed in PylRS gene from Methanosarcina mazei JCM 9314 genome.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.37 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris-HCl (pH 8.5), PEG 200, KCl, MgCl2, sodium citrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97916 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 43994 / % possible obs: 99.7 % / Redundancy: 29 % / Rpim(I) all: 0.01 / Rrim(I) all: 0.053 / Net I/σ(I): 85
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 2174 / Rpim(I) all: 0.138

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2zim

2zim


Resolution: 1.5→37.041 Å / SU ML: 0.13 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 19.18
RfactorNum. reflection% reflection
Rfree0.1962 2217 5.04 %
Rwork0.1635 --
obs0.1651 43991 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→37.041 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2149 0 54 273 2476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052320
X-RAY DIFFRACTIONf_angle_d0.9483139
X-RAY DIFFRACTIONf_dihedral_angle_d17.613918
X-RAY DIFFRACTIONf_chiral_restr0.079338
X-RAY DIFFRACTIONf_plane_restr0.006405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4988-1.53140.23091520.19552544X-RAY DIFFRACTION98
1.5314-1.5670.22541330.18772580X-RAY DIFFRACTION99
1.567-1.60620.20361390.17982566X-RAY DIFFRACTION99
1.6062-1.64960.19921220.17032602X-RAY DIFFRACTION99
1.6496-1.69820.18931280.1742591X-RAY DIFFRACTION99
1.6982-1.7530.21771450.1792592X-RAY DIFFRACTION99
1.753-1.81560.20811410.17312591X-RAY DIFFRACTION100
1.8156-1.88830.21461460.16762620X-RAY DIFFRACTION100
1.8883-1.97420.20711410.16742586X-RAY DIFFRACTION100
1.9742-2.07830.20251240.16842618X-RAY DIFFRACTION100
2.0783-2.20850.18741100.16382657X-RAY DIFFRACTION100
2.2085-2.3790.1911530.16732594X-RAY DIFFRACTION100
2.379-2.61840.18061640.17722619X-RAY DIFFRACTION100
2.6184-2.99710.19261460.16982620X-RAY DIFFRACTION100
2.9971-3.77550.20571390.1512659X-RAY DIFFRACTION100
3.7755-37.05190.18581340.15092735X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2342-0.3949-0.50663.96981.30152.8245-0.05580.1421-0.1512-0.0772-0.0690.27160.1855-0.39460.09880.18690.0250.00120.29350.00270.22014.499728.748550.5386
20.5551-0.0705-0.57710.0646-0.10690.9775-0.1435-0.0667-0.08460.10470.00950.03520.1969-0.13840.17190.1766-0.00510.01420.17290.0050.163719.792118.836143.5676
31.5366-0.1892-0.31680.82190.65361.6293-0.01980.20120.2762-0.1963-0.0126-0.0365-0.3184-0.07780.03490.1858-0.006-0.01560.12210.03270.167131.235434.413618.5015
41.50261.09460.47931.40280.30841.5888-0.07480.06620.0805-0.0063-0.01070.11630.0598-0.19920.10670.10460.0076-0.00660.14120.01090.145919.946225.945719.9917
51.08440.161-0.06650.4860.0361.4594-0.07130.07840.1265-0.04040.02480.0592-0.0779-0.23530.00720.13170.0101-0.0060.14670.00560.16717.941228.566723.5385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 188 through 215 )
2X-RAY DIFFRACTION2chain 'A' and (resid 216 through 256 )
3X-RAY DIFFRACTION3chain 'A' and (resid 257 through 329 )
4X-RAY DIFFRACTION4chain 'A' and (resid 330 through 370 )
5X-RAY DIFFRACTION5chain 'A' and (resid 371 through 454 )

+
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