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- PDB-6ezd: Pyrrolysyl-tRNA synthetase from Canditatus Methanomethylophilus a... -

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Basic information

Entry
Database: PDB / ID: 6ezd
TitlePyrrolysyl-tRNA synthetase from Canditatus Methanomethylophilus alvus (MmaPylRS)
ComponentsPyrrolysyl-tRNA synthetasePyrrolysine—tRNAPyl ligase
KeywordsLIGASE / Pyrrolysyl-tRNA synthetase
Function / homology
Function and homology information


pyrrolysine-tRNAPyl ligase / pyrrolysyl-tRNA synthetase activity
Similarity search - Function
Phenylalanyl tRNA synthetase beta chain, core domain / Phenylalanyl tRNA synthetase beta chain CLM domain / Pyrrolysyl-tRNA ligase, C-terminal / 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) / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Pyrrolysyl-tRNA synthetase
Similarity search - Component
Biological speciesCandidatus Methanomethylophilus alvus Mx1201 1) (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPavkov-Keller, T. / Schweiger, K. / Gruber, K.
Funding support Austria, 1items
OrganizationGrant numberCountry
FFG Austria
CitationJournal: to be published
Title: A new archaeal pyrrolysyl-tRNA synthetase/amber suppressor tRNA pair for orthogonal protein translation
Authors: Fladischer, P. / Blamauer, J. / Pavkov-Keller, T. / Schweiger, K. / Darnhofer, B. / Birner-Gruenberger, R. / Gruber, K. / Wiltschi, B.
History
DepositionNov 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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: Pyrrolysyl-tRNA synthetase
B: Pyrrolysyl-tRNA synthetase
C: Pyrrolysyl-tRNA synthetase
D: Pyrrolysyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)127,2764
Polymers127,2764
Non-polymers00
Water6,557364
1
A: Pyrrolysyl-tRNA synthetase
C: Pyrrolysyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)63,6382
Polymers63,6382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-21 kcal/mol
Surface area24500 Å2
MethodPISA
2
B: Pyrrolysyl-tRNA synthetase
D: Pyrrolysyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)63,6382
Polymers63,6382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-24 kcal/mol
Surface area24340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.642, 94.177, 289.471
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-387-

HOH

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Components

#1: Protein
Pyrrolysyl-tRNA synthetase / Pyrrolysine—tRNAPyl ligase


Mass: 31819.096 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Methanomethylophilus alvus Mx1201 1) (archaea)
Gene: MMALV_11280 / Production host: Escherichia coli (E. coli) / References: UniProt: M9SC49, pyrrolysine-tRNAPyl ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.48 Å3/Da / Density % sol: 50.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.09 M (NaNO3, Na2HPO4, (NH4)2SO4), 0.1 M Tris (base), bicine and 5 mM MgCl2. 15-7mg/ml (in 10 mM HEPES-Na pH 7.4, 300 mM NaCl)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.4→48.78 Å / Num. obs: 49665 / % possible obs: 99 % / Redundancy: 6.4 % / Biso Wilson estimate: 37.17 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.05 / Rrim(I) all: 0.128 / Net I/σ(I): 13.04
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.664 / Num. unique obs: 4856 / CC1/2: 0.772 / Rpim(I) all: 0.277 / Rrim(I) all: 0.721 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DSQ

3dsq


Resolution: 2.4→48.78 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.42
RfactorNum. reflection% reflection
Rfree0.2516 2479 5 %
Rwork0.2149 --
obs0.2167 49571 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8579 0 0 364 8943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038743
X-RAY DIFFRACTIONf_angle_d0.50511792
X-RAY DIFFRACTIONf_dihedral_angle_d7.0555846
X-RAY DIFFRACTIONf_chiral_restr0.0391301
X-RAY DIFFRACTIONf_plane_restr0.0031534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3889-2.43490.3368950.26781814X-RAY DIFFRACTION68
2.4349-2.48460.35171380.2752624X-RAY DIFFRACTION100
2.4846-2.53860.32361410.27322677X-RAY DIFFRACTION100
2.5386-2.59760.32821370.27362594X-RAY DIFFRACTION100
2.5976-2.66260.3561390.28412648X-RAY DIFFRACTION99
2.6626-2.73460.33561350.28532578X-RAY DIFFRACTION98
2.7346-2.8150.27471390.24572642X-RAY DIFFRACTION100
2.815-2.90590.30091390.24662640X-RAY DIFFRACTION100
2.9059-3.00970.28821420.24442684X-RAY DIFFRACTION100
3.0097-3.13020.27011390.22612650X-RAY DIFFRACTION100
3.1302-3.27270.24171390.21822648X-RAY DIFFRACTION100
3.2727-3.44520.29781400.22692647X-RAY DIFFRACTION99
3.4452-3.66090.2791400.22412667X-RAY DIFFRACTION99
3.6609-3.94350.25851380.21452610X-RAY DIFFRACTION98
3.9435-4.34010.21281410.17522689X-RAY DIFFRACTION100
4.3401-4.96760.1951430.16132705X-RAY DIFFRACTION100
4.9676-6.25660.20231440.19842728X-RAY DIFFRACTION100
6.2566-48.7930.18041500.18212847X-RAY DIFFRACTION100

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