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- PDB-4cs3: Catalytic domain of Pyrrolysyl-tRNA synthetase mutant Y306A, Y384... -

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Basic information

Entry
Database: PDB / ID: 4cs3
TitleCatalytic domain of Pyrrolysyl-tRNA synthetase mutant Y306A, Y384F in complex with an adenylated furan-bearing noncanonical amino acid and pyrophosphate
ComponentsPYRROLYSINE--TRNA LIGASE
KeywordsLIGASE / AMINOACYL-TRNA SYNTHETASE / PYRROLYSYL-TRNA-SYNTHETASE / NONCANONICAL AMINO ACIDS / FURANS / CROSSLINKING REACTIONS
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
ADENOSINE MONOPHOSPHATE / 2-(furan-2-yl)ethyl hydrogen carbonate / LYSINE / PYROPHOSPHATE 2- / Pyrrolysine--tRNA ligase
Similarity search - Component
Biological speciesMETHANOSARCINA MAZEI (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.499 Å
AuthorsSchmidt, M.J. / Weber, A. / Pott, M. / Welte, W. / Summerer, D.
Citation
Journal: 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.
#1: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: Red-Light-Controlled Protein-RNA Crosslinking with a Genetically Encoded Furan.
Authors: Schmidt, M.J. / 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

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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)32,6748
Polymers31,7361
Non-polymers9377
Water4,504250
1
A: PYRROLYSINE--TRNA LIGASE
hetero molecules

A: PYRROLYSINE--TRNA LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,34716
Polymers63,4732
Non-polymers1,87414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area9190 Å2
ΔGint-41.1 kcal/mol
Surface area22530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.335, 44.345, 64.165
Angle α, β, γ (deg.)90.00, 99.85, 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 PYRROLYSINE--TRNA LIGASE / PYRROLYSINE--TRNA(PYL) LIGASE / PYRROLYSYL-TRNA SYNTHETASE / PYLRS


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) / Strain (production host): TOP10 / References: UniProt: Q8PWY1, pyrrolysine-tRNAPyl ligase

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Non-polymers , 7 types, 257 molecules

#2: Chemical ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-FU0 / 2-(furan-2-yl)ethyl hydrogen carbonate


Mass: 156.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O4
#5: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsAMP-ESTER OF N-EPSILON-[2-(FURAN-2-YL)ETHOXY]CARBONYL LYSINE: NEW NONCANONICAL AMINO ACID N-EPSILON- ...AMP-ESTER OF N-EPSILON-[2-(FURAN-2-YL)ETHOXY]CARBONYL LYSINE: NEW NONCANONICAL AMINO ACID N-EPSILON-2-FURAN-2-YL ETHOXYCARBONYL LYSINE BOUND TO ADENOSINE-MONOPHOSPHATE

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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: 2.31 Å3/Da / Density % sol: 46.87 % / Description: NONE
Crystal growpH: 8.5
Details: 50 MM TRIS-HCL PH 8.5, 200 MM CALCIUM CHLORIDE, 18 % (W/V) PEG4000

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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: Mar 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→36.49 Å / Num. obs: 45483 / % possible obs: 99.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 21.35 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.12
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.19 / % possible all: 98.6

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Processing

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

Resolution: 1.499→36.489 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 20.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1849 2300 5.1 %
Rwork0.155 --
obs0.1565 45472 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34 Å2
Refinement stepCycle: LAST / Resolution: 1.499→36.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2193 0 57 250 2500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192316
X-RAY DIFFRACTIONf_angle_d1.3423106
X-RAY DIFFRACTIONf_dihedral_angle_d18.106898
X-RAY DIFFRACTIONf_chiral_restr0.075332
X-RAY DIFFRACTIONf_plane_restr0.007398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4986-1.53120.38531400.34152628X-RAY DIFFRACTION98
1.5312-1.56680.30421430.29252679X-RAY DIFFRACTION100
1.5668-1.6060.31091430.26042683X-RAY DIFFRACTION100
1.606-1.64940.26661430.23722692X-RAY DIFFRACTION100
1.6494-1.6980.26791450.22562713X-RAY DIFFRACTION100
1.698-1.75280.24151660.21632642X-RAY DIFFRACTION100
1.7528-1.81540.20371390.19182718X-RAY DIFFRACTION100
1.8154-1.88810.21811390.17182684X-RAY DIFFRACTION100
1.8881-1.9740.16771420.14772700X-RAY DIFFRACTION100
1.974-2.07810.18181490.13982698X-RAY DIFFRACTION100
2.0781-2.20830.15771370.13762690X-RAY DIFFRACTION100
2.2083-2.37870.18361390.13442725X-RAY DIFFRACTION100
2.3787-2.61810.1921290.14082727X-RAY DIFFRACTION99
2.6181-2.99670.1841470.14882710X-RAY DIFFRACTION99
2.9967-3.7750.15311350.14092718X-RAY DIFFRACTION99
3.775-36.49950.16651640.13832765X-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)
10.16030.0274-0.11490.3152-0.03460.0745-0.10150.1255-0.2062-0.1906-0.01470.353-0.0041-0.20870.00320.17910.05590.01110.3486-0.00680.308-33.31428.0650.4138
20.3257-0.16450.05460.0663-0.05890.0904-0.2231-0.4766-0.52480.09570.21560.2660.0673-0.04240.03460.19710.05980.06230.29460.09310.2724-23.86970.882954.1998
3-0.01510.01440.05080.04240.08270.0953-0.0685-0.0266-0.18530.0389-0.01760.02580.1285-0.0893-00.2125-0.00770.0140.168-0.00080.2192-11.2743-4.085631.9159
40.77350.1221-0.16460.20150.16760.7056-0.07830.14110.0968-0.06310.04890.0537-0.1633-0.0474-00.2334-0.0117-0.02310.16350.0120.1938-6.758314.482818.6232
50.53940.25090.14730.06250.00440.3476-0.04450.10750.03890.01720.05280.0194-0.0462-0.22010.00120.2025-0.0125-0.01010.21260.00270.1926-18.10085.253220.2189
60.09110.0043-0.02640.02780.0380.0716-0.1030.06680.22130.0285-0.04330.1033-0.1136-0.091-00.2751-0.0383-0.04760.34070.00860.3341-25.14217.905816.7461
70.04780.02980.04350.10250.09670.0821-0.07050.04780.214-0.11060.03040.1597-0.0633-0.283800.202-0.0024-0.02450.3463-0.00010.2567-25.13687.709717.9535
80.0430.0203-0.00510.0327-0.02940.0284-0.17740.38040.1196-0.23020.10070.1059-0.0329-0.063700.3171-0.0611-0.02180.3020.04560.2114-9.350113.60514.768
90.5029-0.0545-0.01490.1647-0.05630.2222-0.0908-0.078-0.00390.0185-0.00020.0665-0.0541-0.1721-00.17490.01850.01120.22470.00050.1991-20.30766.880737.9208
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 189 THROUGH 215 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 216 THROUGH 236 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 237 THROUGH 256 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 257 THROUGH 329 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 330 THROUGH 370 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 371 THROUGH 384 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 385 THROUGH 402 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 403 THROUGH 416 )
9X-RAY DIFFRACTION9CHAIN A AND (RESID 417 THROUGH 458 )

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