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- PDB-2zwa: Crystal structure of tRNA wybutosine synthesizing enzyme TYW4 -

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Basic information

Entry
Database: PDB / ID: 2zwa
TitleCrystal structure of tRNA wybutosine synthesizing enzyme TYW4
ComponentsLeucine carboxyl methyltransferase 2
KeywordsTRANSFERASE
Function / homology
Function and homology information


tRNAPhe [7-(3-amino-3-carboxypropyl)wyosine37-O]-methyltransferase / tRNAPhe {7-[3-amino-3-(methoxycarbonyl)propyl]wyosine37-N}-methoxycarbonyltransferase / wybutosine biosynthetic process / tRNA methyltransferase activity / tRNA methylation / tRNA modification / mitochondrion / cytoplasm
Similarity search - Function
Methyltransferase Ppm1/Ppm2/Tcmp / Leucine carboxyl methyltransferase / Galactose oxidase, central domain / Kelch-type beta propeller / Galactose oxidase/kelch, beta-propeller / Kelch / Kelch repeat type 1 / Kelch motif / Kelch-type beta propeller / 6 Propeller ...Methyltransferase Ppm1/Ppm2/Tcmp / Leucine carboxyl methyltransferase / Galactose oxidase, central domain / Kelch-type beta propeller / Galactose oxidase/kelch, beta-propeller / Kelch / Kelch repeat type 1 / Kelch motif / Kelch-type beta propeller / 6 Propeller / Neuraminidase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / S-ADENOSYL-L-HOMOCYSTEINE / tRNA wybutosine-synthesizing protein 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsSuzuki, Y. / Noma, A. / Suzuki, T. / Ishitani, R. / Nureki, O.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4.
Authors: Suzuki, Y. / Noma, A. / Suzuki, T. / Ishitani, R. / Nureki, O.
History
DepositionDec 1, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Leucine carboxyl methyltransferase 2
B: Leucine carboxyl methyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,62612
Polymers158,1012
Non-polymers1,52510
Water27,7971543
1
A: Leucine carboxyl methyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,8136
Polymers79,0511
Non-polymers7635
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Leucine carboxyl methyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,8136
Polymers79,0511
Non-polymers7635
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.578, 89.444, 236.286
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Leucine carboxyl methyltransferase 2 / tRNA wybutosine-synthesizing protein 4


Mass: 79050.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PPM2, TYW4, YOL141W / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus
References: UniProt: Q08282, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 1543 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS CONSIDER THAT THIS DIFFERENCE MAY STEM FROM A POLYMORPHISM OF THE YEAST STRAIN OR SOME ...AUTHORS CONSIDER THAT THIS DIFFERENCE MAY STEM FROM A POLYMORPHISM OF THE YEAST STRAIN OR SOME ERROR OF THE YEAST GENOME PROJECT.

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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: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 200mM ammonium citrate (pH 7), 20% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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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 23, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 174812 / Num. obs: 174812 / % possible obs: 98.7 % / Redundancy: 5.5 % / Rsym value: 0.078 / Net I/σ(I): 31.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.37 / Num. unique all: 8086 / Rsym value: 0.344 / % possible all: 92.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→38.619 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.23 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 20.3 / Stereochemistry target values: ML / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.2113 17319 9.91 %Random
Rwork0.17 ---
all0.1742 174754 --
obs0.1742 174754 98.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.833 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso mean: 29.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.3495 Å20 Å20 Å2
2--3.9067 Å20 Å2
3----2.557 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38.619 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10888 0 102 1543 12533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711227
X-RAY DIFFRACTIONf_angle_d1.14215190
X-RAY DIFFRACTIONf_chiral_restr0.081704
X-RAY DIFFRACTIONf_plane_restr0.0051942
X-RAY DIFFRACTIONf_dihedral_angle_d16.8054180
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.703-1.7230.3044770.2644395487283
1.723-1.7430.2925660.2514975554195
1.743-1.7640.2775440.2365103564796
1.764-1.7870.295390.2355184572397
1.787-1.810.2565630.2195124568798
1.81-1.8350.2615550.2175184573998
1.835-1.8610.2695620.2145233579599
1.861-1.8890.2415290.2015220574998
1.889-1.9180.2555960.1975220581699
1.918-1.950.2355770.195230580799
1.95-1.9840.2315530.17952945847100
1.984-2.020.2186100.1755255586599
2.02-2.0580.2346020.18852595861100
2.058-2.10.2335950.17552695864100
2.1-2.1460.2135650.16853045869100
2.146-2.1960.2155730.17153125885100
2.196-2.2510.2125550.16953175872100
2.251-2.3120.235850.16852905875100
2.312-2.380.2276300.16852365866100
2.38-2.4570.2085600.16653605920100
2.457-2.5440.2266000.16653095909100
2.544-2.6460.2246030.17253125915100
2.646-2.7670.2195690.17453275896100
2.767-2.9120.2166250.1753065931100
2.912-3.0950.2085950.16553715966100
3.095-3.3340.2066150.16253505965100
3.334-3.6690.1925780.14554246002100
3.669-4.1990.1575810.13554236004100
4.199-5.2880.175840.13454906074100
5.288-38.6290.1996330.1835359599295

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