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- PDB-6ly7: PylRS C-terminus domain mutant bound with 1-Formyl-L-tryptophan a... -

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Basic information

Entry
Database: PDB / ID: 6ly7
TitlePylRS C-terminus domain mutant bound with 1-Formyl-L-tryptophan 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / N1-FORMYL-TRYPTOPHAN / Pyrrolysine--tRNA ligase / Pyrrolysine--tRNA ligase
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09447266796 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)32,7875
Polymers32,0001
Non-polymers7874
Water2,756153
1
A: Pyrrolysine--tRNA ligase
hetero molecules

A: Pyrrolysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,57310
Polymers63,9992
Non-polymers1,5748
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_985-x+4,-y+3,z1
Unit cell
Length a, b, c (Å)105.346, 105.346, 72.396
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-TRF / N1-FORMYL-TRYPTOPHAN


Type: L-peptide linking / Mass: 232.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12N2O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 3.62 Å3/Da / Density % sol: 66.05 %
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: 2.09→28.3551 Å / Num. obs: 26941 / % possible obs: 96.89 % / Redundancy: 7.3 % / Biso Wilson estimate: 44.2768027561 Å2 / Rpim(I) all: 0.039 / Rrim(I) all: 0.104 / Net I/σ(I): 33.2
Reflection shellResolution: 2.09→2.18 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1908 / Rpim(I) all: 0.308 / Rrim(I) all: 0.829

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Processing

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

2zce


Resolution: 2.09447266796→28.3550953944 Å / SU ML: 0.20472862989 / Cross valid method: FREE R-VALUE / σ(F): 1.35331964804 / Phase error: 19.5171703414
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.183845294 1994 7.40218279011 %
Rwork0.173157246564 24944 -
obs0.173943199964 26938 99.7592860053 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.4604466738 Å2
Refinement stepCycle: LAST / Resolution: 2.09447266796→28.3550953944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2070 0 50 154 2274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009748773399812173
X-RAY DIFFRACTIONf_angle_d1.103421119972935
X-RAY DIFFRACTIONf_chiral_restr0.0613599804269317
X-RAY DIFFRACTIONf_plane_restr0.00701435269154376
X-RAY DIFFRACTIONf_dihedral_angle_d21.4730984138833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0945-2.14680.2516142125311400.2321752864021718X-RAY DIFFRACTION97.3284442116
2.1468-2.20490.2291564778251450.2229676520991783X-RAY DIFFRACTION100
2.2049-2.26970.2307655456551410.2050220887831769X-RAY DIFFRACTION100
2.2697-2.34290.2533534542591390.1946657547941793X-RAY DIFFRACTION100
2.3429-2.42660.2216647594781430.1988498190251753X-RAY DIFFRACTION99.9472851871
2.4266-2.52370.2288353363631400.1947302484341774X-RAY DIFFRACTION99.9477806789
2.5237-2.63850.2371333400551480.2034290504211788X-RAY DIFFRACTION100
2.6385-2.77750.195815676281460.1951479474061786X-RAY DIFFRACTION100
2.7775-2.95140.2181467428971390.2008512421061758X-RAY DIFFRACTION99.947312961
2.9514-3.1790.2095981021911390.1921178037481804X-RAY DIFFRACTION100
3.179-3.49830.1767368800081400.175178201251792X-RAY DIFFRACTION99.8449612403
3.4983-4.00340.1821306454691430.1531839370581796X-RAY DIFFRACTION100
4.0034-5.03920.1376776313641460.133835419151797X-RAY DIFFRACTION100
5.0392-28.355090.1667796148231450.1740536098041833X-RAY DIFFRACTION99.6975806452

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