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- PDB-6abk: Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) comp... -

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Basic information

Entry
Database: PDB / ID: 6abk
TitleCrystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) complexed with TeocLys
ComponentsPyrrolysine--tRNA ligase
KeywordsTRANSLATION / aminoacyl-tRNA synthetase / non-natural amino acids / tRNA / pyrrolysyl-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
Chem-9VF / ADENOSINE-5'-TRIPHOSPHATE / Pyrrolysine--tRNA ligase / Pyrrolysine--tRNA ligase
Similarity search - Component
Biological speciesMethanosarcina mazei JCM 9314 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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 22, 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_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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyrrolysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2036
Polymers31,3471
Non-polymers8575
Water5,332296
1
A: Pyrrolysine--tRNA ligase
hetero molecules

A: Pyrrolysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,40712
Polymers62,6942
Non-polymers1,71310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_856-x+3,y,-z+11
Buried area7060 Å2
ΔGint-77 kcal/mol
Surface area22190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.245, 43.906, 72.451
Angle α, β, γ (deg.)90.00, 118.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Pyrrolysine--tRNA 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, DU43_20175, DU67_18120 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): rosetta
References: UniProt: A0A0F8JXW8, UniProt: Q8PWY1*PLUS, 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-9VF / (2S)-2-azanyl-6-(trimethylsilylmethoxycarbonylamino)hexanoic acid


Type: peptide linking / Mass: 276.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24N2O4Si
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsResidue E444G is a natural mutation observed in PylRS gene from Methanosarcina mazei JCM9314 genome.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris-HCl (pH 8.5), PEG 200, KCl, MgCl2, sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Oct 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 38450 / % possible obs: 99.9 % / Redundancy: 5 % / Rpim(I) all: 0.033 / Rrim(I) all: 0.076 / Net I/σ(I): 26.8
Reflection shellResolution: 1.58→1.62 Å / Num. unique obs: 1888 / Rpim(I) all: 0.205

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Processing

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

2zim


Resolution: 1.58→34.987 Å / SU ML: 0.15 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 18.34
RfactorNum. reflection% reflection
Rfree0.1893 2000 5.2 %
Rwork0.1592 --
obs0.1608 38448 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.58→34.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2156 0 52 296 2504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182323
X-RAY DIFFRACTIONf_angle_d1.9153137
X-RAY DIFFRACTIONf_dihedral_angle_d9.3651976
X-RAY DIFFRACTIONf_chiral_restr0.112333
X-RAY DIFFRACTIONf_plane_restr0.012404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5804-1.61990.26861400.20812564X-RAY DIFFRACTION99
1.6199-1.66370.21831420.18032579X-RAY DIFFRACTION100
1.6637-1.71270.19171410.1662572X-RAY DIFFRACTION100
1.7127-1.7680.21181440.16652612X-RAY DIFFRACTION100
1.768-1.83120.21221420.16712595X-RAY DIFFRACTION100
1.8312-1.90450.19441420.16532588X-RAY DIFFRACTION100
1.9045-1.99110.16121420.15242581X-RAY DIFFRACTION100
1.9911-2.09610.18711430.1542610X-RAY DIFFRACTION100
2.0961-2.22740.18721420.1522602X-RAY DIFFRACTION100
2.2274-2.39940.2291430.15772598X-RAY DIFFRACTION100
2.3994-2.64070.19241440.17142608X-RAY DIFFRACTION100
2.6407-3.02270.20391430.16772615X-RAY DIFFRACTION100
3.0227-3.80750.18251440.14912629X-RAY DIFFRACTION100
3.8075-34.99520.16171480.1532695X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 122.5554 Å / Origin y: 29.9311 Å / Origin z: 27.9423 Å
111213212223313233
T0.0716 Å20.0017 Å2-0.0077 Å2-0.0606 Å20.0089 Å2--0.0747 Å2
L0.4292 °2-0.0402 °20.0366 °2-0.1579 °20.1703 °2--0.3462 °2
S-0.069 Å °0.0515 Å °0.0159 Å °-0.0261 Å °0.0425 Å °0.0286 Å °-0.0198 Å °-0.1019 Å °-0.1065 Å °
Refinement TLS groupSelection details: all

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