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- PDB-5k1p: Catalytic domain of polyspecific pyrrolysyl-tRNA synthetase mutan... -

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Basic information

Entry
Database: PDB / ID: 5k1p
TitleCatalytic domain of polyspecific pyrrolysyl-tRNA synthetase mutant N346A/C348A in complex with AMPPNP
ComponentsPyrrolysine--tRNA ligase
KeywordsLIGASE / protein engineering / aminoacyl-tRNA synthetase / noncanonical 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Pyrrolysine--tRNA ligase
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.499 Å
AuthorsWeber, A.
Funding support United States, Germany, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA161158 United States
National Science Foundation (NSF, United States)CHEM-1148684 United States
Welch FoundationA-1715 United States
German Research Foundation (DFG)SU 726/6-1 Germany
CitationJournal: Chem.Commun.(Camb.) / Year: 2016
Title: Genetically encoded fluorophenylalanines enable insights into the recognition of lysine trimethylation by an epigenetic reader.
Authors: Lee, Y.J. / Schmidt, M.J. / Tharp, J.M. / Weber, A. / Koenig, A.L. / Zheng, H. / Gao, J. / Waters, M.L. / Summerer, D. / Liu, W.R.
History
DepositionMay 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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_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

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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)32,3244
Polymers31,7691
Non-polymers5553
Water4,918273
1
A: Pyrrolysine--tRNA ligase
hetero molecules

A: Pyrrolysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6488
Polymers63,5392
Non-polymers1,1106
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area7170 Å2
ΔGint-53 kcal/mol
Surface area23840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.493, 44.358, 64.314
Angle α, β, γ (deg.)90.00, 99.92, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-833-

HOH

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Components

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


Mass: 31769.412 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP residues 188-454) / Mutation: N346A, C348A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Gene: pylS, MM_1445 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8PWY1, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 47.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 0.2M MgCl2, 0.1M TrisHCl pH9.5, 20% (w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.499→43.281 Å / Num. obs: 44122 / % possible obs: 96 % / Redundancy: 3.3 % / Biso Wilson estimate: 20.54 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.64
Reflection shellResolution: 1.499→1.553 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.03 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(dev_2341: ???)refinement
XDSdata reduction
XDSdata scaling
RefinementStarting model: PDB ID 4CS2

4cs2


Resolution: 1.499→43.281 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.01
RfactorNum. reflection% reflection
Rfree0.196 2221 5.04 %
Rwork0.1652 --
obs0.1668 44049 96.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.84 Å2
Refinement stepCycle: LAST / Resolution: 1.499→43.281 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2198 0 33 273 2504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012311
X-RAY DIFFRACTIONf_angle_d1.13123
X-RAY DIFFRACTIONf_dihedral_angle_d20.5895
X-RAY DIFFRACTIONf_chiral_restr0.079335
X-RAY DIFFRACTIONf_plane_restr0.007404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4993-1.53190.34241350.31312570X-RAY DIFFRACTION95
1.5319-1.56750.30321430.27722666X-RAY DIFFRACTION100
1.5675-1.60670.28071420.25572696X-RAY DIFFRACTION100
1.6067-1.65010.28031450.24472700X-RAY DIFFRACTION100
1.6501-1.69870.2641450.22332719X-RAY DIFFRACTION100
1.6987-1.75350.26561650.2092644X-RAY DIFFRACTION100
1.7535-1.81620.21311420.18712721X-RAY DIFFRACTION100
1.8162-1.88890.2441340.18572706X-RAY DIFFRACTION100
1.8889-1.97490.19891020.19211948X-RAY DIFFRACTION72
1.9749-2.0790.19311520.16132700X-RAY DIFFRACTION99
2.079-2.20930.1811340.15392714X-RAY DIFFRACTION100
2.2093-2.37980.19361160.16272272X-RAY DIFFRACTION83
2.3798-2.61930.20711320.1512739X-RAY DIFFRACTION99
2.6193-2.99820.16591450.15212710X-RAY DIFFRACTION99
2.9982-3.77710.16941220.14672559X-RAY DIFFRACTION93
3.7771-43.29910.17771670.14462764X-RAY DIFFRACTION98

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