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- PDB-6lyb: PylRS C-terminus domain mutant in complex with 3-Benzothienyl-D-a... -

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Basic information

Entry
Database: PDB / ID: 6lyb
TitlePylRS C-terminus domain mutant in complex with 3-Benzothienyl-D-alanine and AMPNP
ComponentsPyrrolysine--tRNA ligase
KeywordsLIGASE / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-EXR / Pyrrolysine--tRNA ligase / Pyrrolysine--tRNA ligase
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.90366470282 Å
AuthorsWeng, J.H. / Tsai, M.D. / Wang, Y.S.
Funding support Taiwan, 3items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-KPQ-109-TPP2 Taiwan
Academia Sinica (Taiwan)AS-KPQ-105-TPP Taiwan
Ministry of Science and Technology (MoST, Taiwan)MOST 107-2113-M-001-025-MY3 Taiwan
CitationJournal: Biochemistry / Year: 2020
Title: Probing the Active Site of Deubiquitinase USP30 with Noncanonical Tryptophan Analogues.
Authors: Jiang, H.K. / Wang, Y.H. / Weng, J.H. / Kurkute, P. / Li, C.L. / Lee, M.N. / Chen, P.J. / Tseng, H.W. / Tsai, M.D. / Wang, Y.S.
History
DepositionFeb 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Derived calculations / Structure summary
Category: audit_author / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.2Nov 29, 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

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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)32,7765
Polymers32,0001
Non-polymers7764
Water2,972165
1
A: Pyrrolysine--tRNA ligase
hetero molecules

A: Pyrrolysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,55110
Polymers63,9992
Non-polymers1,5528
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_785-x+2,-y+3,z1
Buried area7080 Å2
ΔGint-56 kcal/mol
Surface area22520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.369, 105.369, 71.459
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Space group name HallP64
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z

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Components

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


Mass: 31999.602 Da / Num. of mol.: 1 / Fragment: C-terminus domain / Mutation: N346G,C348Q,V401G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Gene: pylS, DU43_20175, DU67_18120 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0F8JXW8, UniProt: Q8PWY1*PLUS, pyrrolysine-tRNAPyl ligase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EXR / (2R)-2-azanyl-3-(1-benzothiophen-3-yl)propanoic acid / 3-(3-Benzothienyl)-D-alanine


Mass: 221.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.82 Å3/Da / Density % sol: 67.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM HEPES , 10% PEG 8000, 10% Ethylene Glycerol

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.9→33.2702 Å / Num. obs: 35444 / % possible obs: 99.95 % / Redundancy: 11.3 % / Biso Wilson estimate: 34.5664072998 Å2 / Rpim(I) all: 0.021 / Rrim(I) all: 0.072 / Net I/σ(I): 41.8
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 2.18 / Num. unique obs: 3515 / Rpim(I) all: 0.276 / Rrim(I) all: 0.911

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.11.1_2575phasing
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZCE

2zce


Resolution: 1.90366470282→33.2701032186 Å / SU ML: 0.205780982514 / Cross valid method: FREE R-VALUE / σ(F): 1.37130760837 / Phase error: 20.2687062321
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.203241286105 2006 5.6596320957 %
Rwork0.177236399035 33438 -
obs0.178676347637 35444 99.9661552347 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.1175964992 Å2
Refinement stepCycle: LAST / Resolution: 1.90366470282→33.2701032186 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2070 0 48 165 2283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01479867621962162
X-RAY DIFFRACTIONf_angle_d1.400893291652920
X-RAY DIFFRACTIONf_chiral_restr0.0828524914555316
X-RAY DIFFRACTIONf_plane_restr0.00868183103352375
X-RAY DIFFRACTIONf_dihedral_angle_d24.0168205996822
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9037-1.95130.30234963731400.2629579104422370X-RAY DIFFRACTION99.7615262321
1.9513-2.0040.2442955103681440.2099670496912365X-RAY DIFFRACTION99.9601593625
2.004-2.0630.2498664136221430.2023828525962378X-RAY DIFFRACTION99.9207292905
2.063-2.12960.2039880957721440.1907218411542377X-RAY DIFFRACTION100
2.1296-2.20570.2200743020111370.1797437040192376X-RAY DIFFRACTION100
2.2057-2.29390.2022171173411440.1813151395492384X-RAY DIFFRACTION100
2.2939-2.39830.2012454040861450.17214289292392X-RAY DIFFRACTION100
2.3983-2.52470.1958754756141450.1750257291252359X-RAY DIFFRACTION100
2.5247-2.68280.2043283463571450.1847185099242395X-RAY DIFFRACTION100
2.6828-2.88990.2328078498111420.1808861161652386X-RAY DIFFRACTION100
2.8899-3.18050.1979724032581440.1831742563282394X-RAY DIFFRACTION100
3.1805-3.64020.2059047939071490.1742989666722400X-RAY DIFFRACTION100
3.6402-4.58440.1834192283011400.1533248720272405X-RAY DIFFRACTION100
4.5844-33.27010.1936751787181440.1816478794882457X-RAY DIFFRACTION99.8847926267

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