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- PDB-4cs2: Catalytic domain of Pyrrolysyl-tRNA synthetase mutant Y306A, Y384... -

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Basic information

Entry
Database: PDB / ID: 4cs2
TitleCatalytic domain of Pyrrolysyl-tRNA synthetase mutant Y306A, Y384F in its apo form
ComponentsPYRROLYSINE--TRNA LIGASE
KeywordsLIGASE
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
DI(HYDROXYETHYL)ETHER / Pyrrolysine--tRNA ligase
Similarity search - Component
Biological speciesMETHANOSARCINA MAZEI (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.1Aug 27, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _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: PYRROLYSINE--TRNA LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0916
Polymers31,7361
Non-polymers3545
Water2,270126
1
A: PYRROLYSINE--TRNA LIGASE
hetero molecules

A: PYRROLYSINE--TRNA LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,18212
Polymers63,4732
Non-polymers70910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5910 Å2
ΔGint-34.1 kcal/mol
Surface area27670 Å2
MethodPQS
Unit cell
Length a, b, c (Å)102.179, 43.492, 63.266
Angle α, β, γ (deg.)90.00, 99.96, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PYRROLYSINE--TRNA 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
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.23 Å3/Da / Density % sol: 44.96 % / Description: NONE
Crystal growpH: 8.5
Details: 50MM TRIS-HCL PH 8.5, 200 MM CALCIUM CHLORIDE AND 18 % (W/V) PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.9→39.92 Å / Num. obs: 21692 / % possible obs: 99.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 31.67 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.75
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.5 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q7E

2q7e


Resolution: 1.9→39.924 Å / SU ML: 0.21 / σ(F): 1.36 / Phase error: 25.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2158 1076 5 %
Rwork0.1777 --
obs0.1796 21678 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.1 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.924 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2065 0 23 126 2214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072134
X-RAY DIFFRACTIONf_angle_d1.0232856
X-RAY DIFFRACTIONf_dihedral_angle_d13.349830
X-RAY DIFFRACTIONf_chiral_restr0.044308
X-RAY DIFFRACTIONf_plane_restr0.005368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.98660.29281340.23922555X-RAY DIFFRACTION99
1.9866-2.09130.26381270.20752556X-RAY DIFFRACTION100
2.0913-2.22230.20861390.19152544X-RAY DIFFRACTION99
2.2223-2.39390.2591280.18932572X-RAY DIFFRACTION99
2.3939-2.63470.28291280.18422581X-RAY DIFFRACTION100
2.6347-3.01590.19731300.17722562X-RAY DIFFRACTION99
3.0159-3.79920.20911350.16772591X-RAY DIFFRACTION99
3.7992-39.93230.19641550.16822641X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0235-3.9423-1.23725.85060.54632.1275-0.254-0.3551-1.11290.23450.05480.96780.2164-0.50920.23290.27560.01160.06030.46570.06270.5193-27.20824.424551.8605
22.33220.5536-0.76111.36440.1784.0927-0.06030.13980.1164-0.13290.10070.0191-0.2265-0.151-0.040.17120.0044-0.02340.22710.01720.3227-8.40169.956721.4126
31.31920.08670.06950.39430.32426.8923-0.06250.07240.0739-0.06740.02850.045-0.2271-0.65320.01110.19310.01140.00640.27630.00920.3251-19.9576.355722.1449
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 189 THROUGH 237 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 238 THROUGH 350 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 351 THROUGH 456 )

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