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- PDB-4cs4: Catalytic domain of Pyrrolysyl-tRNA synthetase mutant Y306A, Y384... -

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Basic information

Entry
Database: PDB / ID: 4cs4
TitleCatalytic domain of Pyrrolysyl-tRNA synthetase mutant Y306A, Y384F in complex with AMPPNP
ComponentsPYRROLYSYL-TRNA SYNTHETASEPyrrolysine—tRNAPyl ligase
KeywordsLIGASE / 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 / Chem-AXZ / PHOSPHATE ION / Pyrrolysine--tRNA ligase
Similarity search - Component
Biological speciesMETHANOSARCINA MAZEI (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.349 Å
AuthorsSchmidt, M.J. / Weber, A. / Pott, M. / Welte, W. / Summerer, D.
CitationJournal: Chembiochem / Year: 2014
Title: Structural Basis of Furan-Amino Acid Recognition by a Polyspecific Aminoacyl-tRNA-Synthetase and its Genetic Encoding in Human Cells.
Authors: Schmidt, M.J. / Weber, A. / Pott, M. / Welte, W. / Summerer, D.
History
DepositionMar 4, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Atomic model
Revision 1.2Aug 27, 2014Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: PYRROLYSYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,91826
Polymers31,7361
Non-polymers2,18125
Water2,198122
1
A: PYRROLYSYL-TRNA SYNTHETASE
hetero molecules

A: PYRROLYSYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,83652
Polymers63,4732
Non-polymers4,36350
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area7160 Å2
ΔGint-48 kcal/mol
Surface area23800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.075, 44.533, 64.359
Angle α, β, γ (deg.)90.00, 99.66, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PYRROLYSYL-TRNA SYNTHETASE / Pyrrolysine—tRNAPyl ligase / PYRROLYSINE--TRNA(PYL) LIGASE / PYRROLYSYL-TRNA SYNTHETASE / PYLRS / PYRROLYSYL-TRNA SYNTHETASE


Mass: 31736.404 Da / Num. of mol.: 1 / Fragment: C-TERMINAL FRAGMENT, RESIDUES 188-454 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOSARCINA MAZEI (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): TOP10 / References: UniProt: Q8PWY1, pyrrolysine-tRNAPyl ligase

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Non-polymers , 6 types, 147 molecules

#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-AXZ / 2-{[dihydroxy(4-aminoethylphenyl)-{4}-sulfanyl]amino}-3-hydroxypropanoic acid


Mass: 290.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N2O5S
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.33 Å3/Da / Density % sol: 47.15 % / Description: NONE
Crystal growpH: 7.5
Details: 100 MM TRIS PH 7.5, 10 % (W/V) PEG 2000 MONOMETHYL ETHER

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→43.1 Å / Num. obs: 62528 / % possible obs: 99.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 20.28 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.67
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 3 % / Rmerge(I) obs: 1.42 / Mean I/σ(I) obs: 0.74 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.349→43.1 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 20.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1756 3163 5.1 %
Rwork0.1483 --
obs0.1497 62511 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.5 Å2
Refinement stepCycle: LAST / Resolution: 1.349→43.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2173 0 135 122 2430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0222369
X-RAY DIFFRACTIONf_angle_d1.3383146
X-RAY DIFFRACTIONf_dihedral_angle_d14.565915
X-RAY DIFFRACTIONf_chiral_restr0.08334
X-RAY DIFFRACTIONf_plane_restr0.007400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3492-1.36940.43181310.41112458X-RAY DIFFRACTION96
1.3694-1.39070.41681370.35922560X-RAY DIFFRACTION99
1.3907-1.41360.38761330.33352506X-RAY DIFFRACTION99
1.4136-1.43790.38021380.32462610X-RAY DIFFRACTION100
1.4379-1.46410.33131370.27872565X-RAY DIFFRACTION100
1.4641-1.49220.33121360.25142557X-RAY DIFFRACTION100
1.4922-1.52270.24411390.22742581X-RAY DIFFRACTION100
1.5227-1.55580.24421360.20452554X-RAY DIFFRACTION99
1.5558-1.5920.23321390.19622624X-RAY DIFFRACTION100
1.592-1.63180.2441380.18572583X-RAY DIFFRACTION100
1.6318-1.67590.22091350.17952549X-RAY DIFFRACTION100
1.6759-1.72530.21751360.14952574X-RAY DIFFRACTION100
1.7253-1.78090.17661630.14182588X-RAY DIFFRACTION100
1.7809-1.84460.1581280.13462569X-RAY DIFFRACTION100
1.8446-1.91850.18361420.12342603X-RAY DIFFRACTION100
1.9185-2.00580.16121400.11152594X-RAY DIFFRACTION100
2.0058-2.11150.13211290.11082579X-RAY DIFFRACTION100
2.1115-2.24380.13531420.11062581X-RAY DIFFRACTION99
2.2438-2.4170.14571290.11472605X-RAY DIFFRACTION100
2.417-2.66020.17611290.12392612X-RAY DIFFRACTION100
2.6602-3.04510.14991320.12662615X-RAY DIFFRACTION100
3.0451-3.83610.14661340.13492610X-RAY DIFFRACTION99
3.8361-43.12190.16991600.16382671X-RAY DIFFRACTION99

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