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- PDB-2zio: Crystal structure of the catalytic domain of pyrrolysyl-tRNA synt... -

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Basic information

Entry
Database: PDB / ID: 2zio
TitleCrystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with AlocLys-AMP and PNP
ComponentsPyrrolysyl-tRNA synthetase
KeywordsLIGASE / aminoacyl-tRNA synthetase / pyrrolysyl-tRNA synthetase / tRNA / pyrrolysine / ATP analogue / non-natural amino acid / unnatural amino acid / ATP-binding / Cytoplasm / Nucleotide-binding / Protein biosynthesis / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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
IMIDODIPHOSPHORIC ACID / Chem-AYB / Pyrrolysine--tRNA ligase
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsYanagisawa, T. / Ishii, R. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Chem.Biol. / Year: 2008
Title: Multistep Engineering of Pyrrolysyl-tRNA Synthetase to Genetically Encode N(varepsilon)-(o-Azidobenzyloxycarbonyl) lysine for Site-Specific Protein Modification
Authors: Yanagisawa, T. / Ishii, R. / Fukunaga, R. / Kobayashi, T. / Sakamoto, K. / Yokoyama, S.
History
DepositionFeb 19, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyrrolysyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0833
Polymers33,3441
Non-polymers7382
Water2,738152
1
A: Pyrrolysyl-tRNA synthetase
hetero molecules

A: Pyrrolysyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1656
Polymers66,6882
Non-polymers1,4774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area5340 Å2
ΔGint-18.8 kcal/mol
Surface area23030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.150, 104.150, 71.060
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

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


Mass: 33344.164 Da / Num. of mol.: 1 / Fragment: C-terminal fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Strain: JCM9314 / Gene: pylS / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q8PWY1, pyrrolysine-tRNAPyl ligase
#2: Chemical ChemComp-2PN / IMIDODIPHOSPHORIC ACID


Mass: 176.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H5NO6P2
#3: Chemical ChemComp-AYB / 5'-O-[(S)-({(2S)-2-amino-6-[(propoxycarbonyl)amino]hexanoyl}oxy)(hydroxy)phosphoryl]adenosine / NE-ALLYLOXYCARBONYL-L-LYSINE-5'-ADENOSINE MONOPHOSPHATE


Mass: 561.483 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H32N7O10P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONFLICT IS DUE TO THE STRAIN DIFFERENCE (JCM9314 AND GOE1).

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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: 3.34 Å3/Da / Density % sol: 63.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Na/Cacodylate, MgCl2, PEG3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 26977 / % possible obs: 98.9 % / Redundancy: 8.5 % / Biso Wilson estimate: 29.3 Å2 / Rsym value: 0.059
Reflection shellResolution: 2.06→2.1 Å / Redundancy: 4.7 % / Rsym value: 0.339 / % possible all: 82.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WK3

1wk3
PDB Unreleased entry


Resolution: 2.06→42 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1664781.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2681 9.9 %RANDOM
Rwork0.183 ---
obs0.183 26965 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.3507 Å2 / ksol: 0.357135 e/Å3
Displacement parametersBiso mean: 52.2 Å2
Baniso -1Baniso -2Baniso -3
1--3.84 Å20.47 Å20 Å2
2---3.84 Å20 Å2
3---7.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.06→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2074 0 47 152 2273
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d2.08
X-RAY DIFFRACTIONc_mcbond_it4.71.5
X-RAY DIFFRACTIONc_mcangle_it6.372
X-RAY DIFFRACTIONc_scbond_it7.312
X-RAY DIFFRACTIONc_scangle_it9.522.5
LS refinement shellResolution: 2.06→2.19 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.308 433 10.2 %
Rwork0.264 3816 -
obs--94.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4ligand5.paramligand5.top

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