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- PDB-6ab8: Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) comp... -

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Basic information

Entry
Database: PDB / ID: 6ab8
TitleCrystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) complexed with ZLys
ComponentsPyrrolysine--tRNA ligase
KeywordsTRANSLATION / aminoacyl-tRNA synthetase / pyrrolysyl-tRNA synthetase / tRNA / 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-9VC / 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: 1.753 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 20, 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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.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

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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)32,5669
Polymers31,3471
Non-polymers1,2198
Water3,657203
1
A: Pyrrolysine--tRNA ligase
hetero molecules

A: Pyrrolysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,13218
Polymers62,6942
Non-polymers2,43816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area7790 Å2
ΔGint-80 kcal/mol
Surface area22580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.134, 43.893, 62.070
Angle α, β, γ (deg.)90.00, 98.83, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 211 molecules

#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-9VC / (2S)-2-azanyl-6-(phenylmethoxycarbonylamino)hexanoic acid


Type: peptide linking / Mass: 280.320 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N2O4
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.2 Å3/Da / Density % sol: 43.98 %
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: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 27397 / % possible obs: 99.6 % / Redundancy: 3.7 % / Rpim(I) all: 0.046 / Rrim(I) all: 0.089 / Net I/σ(I): 19.1
Reflection shellResolution: 1.75→1.79 Å / Num. unique obs: 1346 / Rpim(I) all: 0.352

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2zim

2zim


Resolution: 1.753→42.283 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 21.35
RfactorNum. reflection% reflection
Rfree0.2131 1997 7.29 %
Rwork0.1722 --
obs0.1752 27388 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.753→42.283 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2132 0 76 203 2411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112310
X-RAY DIFFRACTIONf_angle_d1.1493122
X-RAY DIFFRACTIONf_dihedral_angle_d6.0772499
X-RAY DIFFRACTIONf_chiral_restr0.074334
X-RAY DIFFRACTIONf_plane_restr0.008403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7526-1.79640.26291390.23621762X-RAY DIFFRACTION96
1.7964-1.8450.30931390.21921777X-RAY DIFFRACTION99
1.845-1.89930.24561430.18911821X-RAY DIFFRACTION100
1.8993-1.96060.22731370.17451762X-RAY DIFFRACTION99
1.9606-2.03070.22861430.17631806X-RAY DIFFRACTION99
2.0307-2.1120.21021420.17461810X-RAY DIFFRACTION100
2.112-2.20810.2141440.16751831X-RAY DIFFRACTION100
2.2081-2.32450.1941420.16751807X-RAY DIFFRACTION100
2.3245-2.47010.21441420.17571806X-RAY DIFFRACTION100
2.4701-2.66080.23161430.18521813X-RAY DIFFRACTION100
2.6608-2.92850.23741460.18631852X-RAY DIFFRACTION100
2.9285-3.35220.22451430.17621811X-RAY DIFFRACTION100
3.3522-4.22280.19031450.14271850X-RAY DIFFRACTION100
4.2228-42.29480.1911490.17121883X-RAY DIFFRACTION99

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