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- PDB-6ly6: PylRS C-terminus domain mutant bound with 3-(1-Naphthyl)-L-alanin... -

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Basic information

Entry
Database: PDB / ID: 6ly6
TitlePylRS C-terminus domain mutant bound with 3-(1-Naphthyl)-L-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 / Pyrrolysyl-tRNA ligase, C-terminal / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / 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)
Similarity search - Domain/homology
NAPHTHALEN-2-YL-3-ALANINE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Pyrrolysine--tRNA ligase / Pyrrolysine--tRNA ligase
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.50013285673 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)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)32,7705
Polymers32,0001
Non-polymers7704
Water1,20767
1
A: Pyrrolysine--tRNA ligase
hetero molecules

A: Pyrrolysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,53910
Polymers63,9992
Non-polymers1,5408
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area7260 Å2
ΔGint-52 kcal/mol
Surface area22410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.723, 105.723, 71.597
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 / 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-ALN / NAPHTHALEN-2-YL-3-ALANINE


Type: L-peptide linking / Mass: 215.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 3.85 Å3/Da / Density % sol: 68.07 %
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: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→28.201 Å / Num. obs: 15881 / % possible obs: 98.96 % / Redundancy: 10.6 % / Biso Wilson estimate: 46.2538928928 Å2 / Rpim(I) all: 0.029 / Rrim(I) all: 0.094 / Net I/σ(I): 38.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 1581 / Rpim(I) all: 0.171 / Rrim(I) all: 0.513

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Processing

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

2zce


Resolution: 2.50013285673→26.43075 Å / SU ML: 0.257518026885 / Cross valid method: FREE R-VALUE / σ(F): 1.34760112684 / Phase error: 19.4376352925
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.191717684171 1573 9.90491782633 %
Rwork0.177338201625 14308 -
obs0.178766103593 15881 99.9874079204 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.2116976936 Å2
Refinement stepCycle: LAST / Resolution: 2.50013285673→26.43075 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2092 0 49 67 2208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009427022285522194
X-RAY DIFFRACTIONf_angle_d1.213208327262959
X-RAY DIFFRACTIONf_chiral_restr0.0725725139975319
X-RAY DIFFRACTIONf_plane_restr0.00858677695534378
X-RAY DIFFRACTIONf_dihedral_angle_d27.00381577821389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.500133-2.58080.2552607411241470.225412146231298X-RAY DIFFRACTION100
2.5808-2.67290.2307374761311400.1953920310941268X-RAY DIFFRACTION99.9290276792
2.6729-2.77980.2635461184191430.1901608514811319X-RAY DIFFRACTION100
2.7798-2.90620.195878436321370.1982732232921283X-RAY DIFFRACTION100
2.9062-3.05920.2373758823651390.2053529273391295X-RAY DIFFRACTION100
3.0592-3.25050.2257627474411410.2091356006051294X-RAY DIFFRACTION100
3.2505-3.5010.2162629645511390.1915545268641299X-RAY DIFFRACTION100
3.501-3.85240.1728402440411500.176885717651304X-RAY DIFFRACTION100
3.8524-4.40760.181024440751430.1532265671561306X-RAY DIFFRACTION100
4.4076-5.54460.1435589673151500.1380075630691308X-RAY DIFFRACTION100
5.5446-26.430750.1848364265941440.1848964749981334X-RAY DIFFRACTION100

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