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- PDB-3qtc: Crystal structure of the catalytic domain of MmOmeRS, an O-methyl... -

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Basic information

Entry
Database: PDB / ID: 3qtc
TitleCrystal structure of the catalytic domain of MmOmeRS, an O-methyl tyrosyl-tRNA synthetase evolved from Methanosarcina mazei PylRS, complexed with O-methyl tyrosine and AMP-PNP
ComponentsPyrrolysyl-tRNA synthetase
KeywordsLIGASE / pyrrolysyl-tRNA synthetase / aminoacyl-tRNA synthetase / ATP binding / O-methyl tyrosine binding / magnesium binding / aminoacylation / esterification
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
O-methyl-L-tyrosine / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Pyrrolysine--tRNA ligase
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsDellas, N. / Takimoto, J.K. / Noel, J.P. / Wang, L.
CitationJournal: Acs Chem.Biol. / Year: 2011
Title: Stereochemical Basis for Engineered Pyrrolysyl-tRNA Synthetase and the Efficient in Vivo Incorporation of Structurally Divergent Non-native Amino Acids.
Authors: Takimoto, J.K. / Dellas, N. / Noel, J.P. / Wang, L.
History
DepositionFeb 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Sep 13, 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 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyrrolysyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,55610
Polymers33,4951
Non-polymers1,0609
Water4,234235
1
A: Pyrrolysyl-tRNA synthetase
hetero molecules

A: Pyrrolysyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,11220
Polymers66,9912
Non-polymers2,12118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1,-y-1,z1
Buried area9170 Å2
ΔGint-19 kcal/mol
Surface area22730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.809, 104.809, 71.674
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 33495.391 Da / Num. of mol.: 1 / Fragment: catalytic domain of PylRS, UNP residues 185-454 / Mutation: A302T, N346V, C348W, Y384F, V401L
Source method: isolated from a genetically manipulated source
Details: gene was evolved (in the context of the Y384F mutant) and found to have the following mutations: A302T, N346V, C348W, V401L
Source: (gene. exp.) Methanosarcina mazei (archaea) / Gene: MM_1445, pylS / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8PWY1, pyrrolysine-tRNAPyl ligase

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Non-polymers , 5 types, 244 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-0A1 / O-methyl-L-tyrosine


Type: L-peptide linking / Mass: 195.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13NO3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 3.39 Å3/Da / Density % sol: 63.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 11% PEG MME 2000, 100mM TRIS-HCl pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 13, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 45085 / Num. obs: 44965 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 35.266 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 35.06
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
1.75-1.866.40.3824.26455587238716198.9
1.86-1.9910.80.20211.047354868356835100
1.99-2.14110.10920.696997863366335100
2.14-2.3511.20.07131.696566458675867100
2.35-2.6311.20.04944.045913552995298100
2.63-3.03110.03756.795153746824682100
3.03-3.7110.80.03169.654268039643964100
3.71-5.2210.70.02678.593314831033103100
5.22-5010.20.02478.19175911761172097.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.05 Å45.38 Å
Translation2.05 Å45.38 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZCE

2zce


Resolution: 1.75→42.3 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.2133 / WRfactor Rwork: 0.187 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8712 / SU B: 1.741 / SU ML: 0.057 / SU R Cruickshank DPI: 0.0896 / SU Rfree: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2124 2268 5 %RANDOM
Rwork0.1834 ---
obs0.1849 44961 99.78 %-
all-45085 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 85.56 Å2 / Biso mean: 29.9312 Å2 / Biso min: 16.35 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.75→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2102 0 67 235 2404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222271
X-RAY DIFFRACTIONr_angle_refined_deg1.3052.0163065
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7935272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94723.636110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38115419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1891521
X-RAY DIFFRACTIONr_chiral_restr0.0860.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211713
X-RAY DIFFRACTIONr_mcbond_it0.7741.51324
X-RAY DIFFRACTIONr_mcangle_it1.48822150
X-RAY DIFFRACTIONr_scbond_it2.0833947
X-RAY DIFFRACTIONr_scangle_it3.5834.5911
LS refinement shellResolution: 1.752→1.798 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 176 -
Rwork0.278 3100 -
all-3276 -
obs--98.26 %

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