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- PDB-4kgn: Crystal structure of a tRNA (cytidine(34)-2'-O)-methyltransferase... -

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Basic information

Entry
Database: PDB / ID: 4kgn
TitleCrystal structure of a tRNA (cytidine(34)-2'-O)-methyltransferase bound to S-adenosyl homocysteine
ComponentstRNA (cytidine(34)-2'-O)-methyltransferase
KeywordsTRANSFERASE / Structural Genomics / NIAID / Seattle Structural Genomics Center for Infectious Disease / SSGCID / National Institute for Allergy and Infectious Disease / tRNA methyltransferase / trefoil protein knot / 3(1) protein knot / S-adenosyl-methionine-dependent / SAM / S-adenosylhomocysteine / SAH / half-site occupancy
Function / homology
Function and homology information


wobble position cytosine ribose methylation / wobble position uridine ribose methylation / tRNA (cytidine(34)-2'-O)-methyltransferase activity / tRNA (5-carboxymethylaminomethyluridine(34)-2'-O)-methyltransferase activity / tRNA (cytidine34-2'-O)-methyltransferase / RNA binding / cytoplasm
Similarity search - Function
tRNA (cytidine/uridine-2'-O-)-methyltransferase / tRNA/rRNA methyltransferase, SpoU type / SpoU rRNA Methylase family / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / tRNA (cytidine(34)-2'-O)-methyltransferase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of a TrmH family tRNA methyltransferase bound to S-adenosyl homocysteine
Authors: Edwards, T.E. / Fairman, J.W. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionApr 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _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: tRNA (cytidine(34)-2'-O)-methyltransferase
B: tRNA (cytidine(34)-2'-O)-methyltransferase
C: tRNA (cytidine(34)-2'-O)-methyltransferase
D: tRNA (cytidine(34)-2'-O)-methyltransferase
E: tRNA (cytidine(34)-2'-O)-methyltransferase
F: tRNA (cytidine(34)-2'-O)-methyltransferase
G: tRNA (cytidine(34)-2'-O)-methyltransferase
H: tRNA (cytidine(34)-2'-O)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,93518
Polymers142,1858
Non-polymers1,75010
Water7,710428
1
A: tRNA (cytidine(34)-2'-O)-methyltransferase
B: tRNA (cytidine(34)-2'-O)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0025
Polymers35,5462
Non-polymers4553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-35 kcal/mol
Surface area12740 Å2
MethodPISA
2
C: tRNA (cytidine(34)-2'-O)-methyltransferase
D: tRNA (cytidine(34)-2'-O)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9664
Polymers35,5462
Non-polymers4202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-19 kcal/mol
Surface area13440 Å2
MethodPISA
3
E: tRNA (cytidine(34)-2'-O)-methyltransferase
F: tRNA (cytidine(34)-2'-O)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0025
Polymers35,5462
Non-polymers4553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-32 kcal/mol
Surface area13560 Å2
MethodPISA
4
G: tRNA (cytidine(34)-2'-O)-methyltransferase
H: tRNA (cytidine(34)-2'-O)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9664
Polymers35,5462
Non-polymers4202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-22 kcal/mol
Surface area13160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.600, 149.710, 80.300
Angle α, β, γ (deg.)90.00, 90.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
tRNA (cytidine(34)-2'-O)-methyltransferase / tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmL


Mass: 17773.127 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: BURPS1710b_0668, trmL / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli)
References: UniProt: Q3JWH1, tRNA (cytidine34-2'-O)-methyltransferase
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.22 Å3/Da / Density % sol: 44.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: BupsA.00072.a.A1 PW25076 at 25 mg/mL with 3 mM SAH against Morpheus screen condition G12, 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.02 M each carboxylate: sodium formate, ammonium ...Details: BupsA.00072.a.A1 PW25076 at 25 mg/mL with 3 mM SAH against Morpheus screen condition G12, 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.02 M each carboxylate: sodium formate, ammonium acetate, trisodium citrate, sodium potassium L-tartrate, sodium oxamate, 0.1 M bicine/Trizma pH 8.5, crystal tracking ID 236960g12, unique puck ID qoj5-3, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.889
11-h,-k,l20.111
ReflectionResolution: 2.15→50 Å / Num. all: 67356 / Num. obs: 66051 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 13.84
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.15-2.210.4612.92197.4
2.21-2.270.3743.55197.3
2.27-2.330.314.28197.7
2.33-2.40.2575.17197.7
2.4-2.480.2196.11197.7
2.48-2.570.1887.05198
2.57-2.670.168.27198.2
2.67-2.780.1389.58198.1
2.78-2.90.10911.66198.2
2.9-3.040.09313.61198.2
3.04-3.210.07217.06198.1
3.21-3.40.0619.95198.3
3.4-3.630.04824.32198
3.63-3.930.04326.45198.7
3.93-4.30.03829.35198.5
4.3-4.810.03532.71198.7
4.81-5.550.03432198.9
5.55-6.80.03629.63199.4
6.8-9.620.02932.99199.3
9.620.02737.15197.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å44.17 Å
Translation3 Å44.17 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→44.17 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 7.872 / SU ML: 0.105 / SU R Cruickshank DPI: 0.2468 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19333 3346 5.1 %RANDOM
Rwork0.1692 ---
obs0.17043 62704 95.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.742 Å2
Baniso -1Baniso -2Baniso -3
1-11.72 Å20 Å2-7.22 Å2
2---0.09 Å2-0 Å2
3----11.63 Å2
Refinement stepCycle: LAST / Resolution: 2.15→44.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9167 0 110 428 9705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0199558
X-RAY DIFFRACTIONr_bond_other_d0.0010.028646
X-RAY DIFFRACTIONr_angle_refined_deg1.421.95113075
X-RAY DIFFRACTIONr_angle_other_deg0.789319676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85151211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4122.692442
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.379151209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3581581
X-RAY DIFFRACTIONr_chiral_restr0.080.21402
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111197
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022390
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1941.8654883
X-RAY DIFFRACTIONr_mcbond_other1.1941.8654882
X-RAY DIFFRACTIONr_mcangle_it1.9942.7876078
X-RAY DIFFRACTIONr_scbond_it1.3031.894675
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.133→2.188 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 184 -
Rwork0.2 3178 -
obs--65.66 %
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)
11.9030.2782-0.48481.4043-0.39561.30010.04120.03290.0280.0203-0.072-0.1899-0.02310.15740.03080.00530.00680.01650.07230.00810.146629.55597.44540.6791
20.94490.22610.11631.9241-0.68611.7142-0.0404-0.10160.03810.32440.10970.2185-0.1908-0.0812-0.06930.07590.01470.06330.051-0.00050.12328.89496.072413.0072
31.61140.61590.34672.30420.10721.17040.04080.01470.07420.00130.03080.28580.1148-0.1345-0.07170.049-0.03090.0230.07670.03140.1539-0.7465-32.76627.3643
41.13820.19780.20982.66660.13671.4386-0.0277-0.0059-0.09990.2250.1138-0.2580.10610.0777-0.08610.0640.01220.01940.0575-0.00380.143120.2323-26.942617.1948
51.7698-0.5558-0.621.99780.57881.47540.08070.08640.0004-0.1137-0.02780.2642-0.1241-0.1645-0.05280.02790.03280.01050.10760.02370.1661-0.46775.639-25.329
60.7803-0.05030.08911.75990.24112.2054-0.07520.00450.0965-0.21050.1378-0.1307-0.16490.1324-0.06270.0649-0.00570.02270.0630.00560.12920.65610.4088-35.5196
72.56360.43730.74971.83950.54021.00820.1538-0.0508-0.07110.0828-0.13430.15340.0679-0.1731-0.01940.0354-0.01440.02340.0584-0.00060.12722.642439.648520.3517
81.36020.12160.19071.92920.38111.89430.0555-0.1356-0.08060.36140.0481-0.25710.16590.1487-0.10360.10180.0004-0.03050.0632-0.00890.146843.451341.617731.5375
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 156
2X-RAY DIFFRACTION1A201 - 202
3X-RAY DIFFRACTION2B1 - 156
4X-RAY DIFFRACTION3C0 - 156
5X-RAY DIFFRACTION3C201 - 202
6X-RAY DIFFRACTION4D-1 - 156
7X-RAY DIFFRACTION5E1 - 156
8X-RAY DIFFRACTION5E201 - 202
9X-RAY DIFFRACTION6F-1 - 156
10X-RAY DIFFRACTION7G1 - 156
11X-RAY DIFFRACTION7G201 - 202
12X-RAY DIFFRACTION8H1 - 156

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