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

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Basic information

Entry
Database: PDB / ID: 6abl
TitleCrystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) complexed with oBrZLys
ComponentsPyrrolysine--tRNA ligase
KeywordsTRANSLATION / aminoacyl-tRNA synthetase / non-natural amino acids / pyrrolysyl-tRNA synthetase / tRNA
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-9VL / ADENOSINE-5'-TRIPHOSPHATE / Pyrrolysine--tRNA ligase
Similarity search - Component
Biological speciesMethanosarcina mazei JCM 9314 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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

Downloads & links

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Assembly

Deposited unit
A: Pyrrolysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2866
Polymers31,3471
Non-polymers9395
Water5,621312
1
A: Pyrrolysine--tRNA ligase
hetero molecules

A: Pyrrolysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,57312
Polymers62,6942
Non-polymers1,87910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area7110 Å2
ΔGint-75 kcal/mol
Surface area22500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.671, 44.281, 72.654
Angle α, β, γ (deg.)90.00, 118.43, 90.00
Int Tables number5
Space group name H-MC121

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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-9VL / (2S)-2-azanyl-6-[(2-bromophenyl)methoxycarbonylamino]hexanoic acid


Type: peptide linking / Mass: 359.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19BrN2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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.

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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: 2.29 Å3/Da / Density % sol: 46.38 %
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Jul 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.47→50 Å / Num. obs: 48022 / % possible obs: 98.9 % / Redundancy: 4.1 % / Rpim(I) all: 0.032 / Rrim(I) all: 0.066 / Net I/σ(I): 33
Reflection shellResolution: 1.47→1.51 Å / Num. unique obs: 2369 / Rpim(I) all: 0.252

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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: 1.47→35.061 Å / SU ML: 0.14 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 19.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1929 2000 4.16 %
Rwork0.1567 --
obs0.1582 48022 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.47→35.061 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2156 0 55 312 2523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132339
X-RAY DIFFRACTIONf_angle_d1.4613169
X-RAY DIFFRACTIONf_dihedral_angle_d17.913934
X-RAY DIFFRACTIONf_chiral_restr0.104341
X-RAY DIFFRACTIONf_plane_restr0.009409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.50680.26721380.22813180X-RAY DIFFRACTION97
1.5068-1.54750.23041420.19433267X-RAY DIFFRACTION98
1.5475-1.59310.20811390.17933212X-RAY DIFFRACTION98
1.5931-1.64450.21431430.17663277X-RAY DIFFRACTION98
1.6445-1.70330.21061420.1733266X-RAY DIFFRACTION99
1.7033-1.77150.2211430.17643272X-RAY DIFFRACTION99
1.7715-1.85210.20011420.17113276X-RAY DIFFRACTION99
1.8521-1.94970.2311410.16423259X-RAY DIFFRACTION99
1.9497-2.07190.17011440.16583304X-RAY DIFFRACTION99
2.0719-2.23180.221440.15533324X-RAY DIFFRACTION100
2.2318-2.45640.20431440.15823315X-RAY DIFFRACTION100
2.4564-2.81170.20581460.16993334X-RAY DIFFRACTION100
2.8117-3.54190.19071450.14973354X-RAY DIFFRACTION100
3.5419-35.07080.16181470.13623382X-RAY DIFFRACTION98
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)
13.85290.341-0.92082.73710.04863.9695-0.13530.191-0.1687-0.01840.01480.20160.4038-0.48550.15030.19780.01950.00230.31660.01120.207856.32611.43351.314
27.7184-3.9955-2.63352.16711.48610.9711-0.3681-0.2632-0.45050.27110.12080.27090.2545-0.10610.30380.26450.04110.05890.2670.06690.219266.2773.39354.268
31.7161-0.34690.60290.89950.6478.079-0.0657-0.0857-0.17320.11-0.04180.05290.3462-0.22810.18030.127-0.02610.01730.09730.0110.171878.606-0.50331.516
41.6381-0.1099-0.23681.90450.35232.3201-0.05250.21330.4217-0.17690.05820.2356-0.5154-0.1339-0.00350.2431-0.0075-0.01380.16070.05320.269581.11819.70319.14
52.0808-0.5469-0.71142.12960.7392.4749-0.00980.24450.1937-0.16280.01-0.0417-0.3222-0.1027-0.03630.1698-0.0222-0.02520.14130.02410.14983.79916.22919.146
61.38880.94510.10031.28120.0461.5334-0.10330.12830.0699-0.06250.03550.14930.0121-0.21430.04140.11330.0039-0.02470.15760.01580.165571.6978.52720.622
71.110.2247-0.27040.55290.00872.0536-0.11230.09120.0856-0.05650.06730.0993-0.1107-0.2634-0.01690.14360.0113-0.00950.1620.00530.190269.7411.16223.981
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 237 )
3X-RAY DIFFRACTION3chain 'A' and (resid 238 through 256 )
4X-RAY DIFFRACTION4chain 'A' and (resid 257 through 284 )
5X-RAY DIFFRACTION5chain 'A' and (resid 285 through 329 )
6X-RAY DIFFRACTION6chain 'A' and (resid 330 through 370 )
7X-RAY DIFFRACTION7chain 'A' and (resid 371 through 454 )

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