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- PDB-3e5y: Crystal structure of TrmH family RNA methyltransferase from Burkh... -

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Basic information

Entry
Database: PDB / ID: 3e5y
TitleCrystal structure of TrmH family RNA methyltransferase from Burkholderia pseudomallei
ComponentsTrmH family RNA methyltransferase
KeywordsTRANSFERASE / SSGCID / protein knot / deCODE / RNA methyltransferase / Methyltransferase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


tRNA (cytidine34-2'-O)-methyltransferase / tRNA methyltransferase activity / S-adenosylmethionine-dependent methyltransferase activity / 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
tRNA (cytidine(34)-2'-O)-methyltransferase / tRNA (cytidine(34)-2'-O)-methyltransferase
Similarity search - Component
Biological speciesBurkholderia pseudomallei 305 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of TrmH family RNA methyltransferase from Burkholderia pseudomallei
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionAug 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TrmH family RNA methyltransferase
B: TrmH family RNA methyltransferase


Theoretical massNumber of molelcules
Total (without water)35,5462
Polymers35,5462
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-8 kcal/mol
Surface area13260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.724, 80.532, 80.882
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 TrmH family RNA methyltransferase / RNA methyltransferase / TrmH family / group 2


Mass: 17773.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei 305 (bacteria)
Gene: BURPS305_4843 / Production host: Escherichia coli (E. coli) / References: UniProt: A4LJP7, UniProt: A0A0E1SBH3*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.14 Å3/Da / Density % sol: 42.54 %
Crystal growTemperature: 289 K / pH: 8.5
Details: PACT sparse matrix screen G10 and H10; 20% PEG 3350, 0.2 M sodium/potassium phosphate, 0.1 M BisTris propane, pH 7.5 or 8.5; 27.6 mg/mL protein; Crystal ID 109613h10, VAPOR DIFFUSION, ...Details: PACT sparse matrix screen G10 and H10; 20% PEG 3350, 0.2 M sodium/potassium phosphate, 0.1 M BisTris propane, pH 7.5 or 8.5; 27.6 mg/mL protein; Crystal ID 109613h10, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 2, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 12194 / % possible obs: 97.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 12
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 3 / % possible all: 95.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.4.0067refinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J85

1j85


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 8.678 / SU ML: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.669 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 592 4.9 %RANDOM
Rwork0.213 ---
obs0.215 12162 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.83 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å20 Å20 Å2
2---0.97 Å20 Å2
3---2.61 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2329 0 0 162 2491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222407
X-RAY DIFFRACTIONr_bond_other_d0.0020.021690
X-RAY DIFFRACTIONr_angle_refined_deg1.7241.943272
X-RAY DIFFRACTIONr_angle_other_deg1.47534025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.2445294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.17821.825126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.96915350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6121532
X-RAY DIFFRACTIONr_chiral_restr0.0880.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212756
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02570
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_it0.8461.51483
X-RAY DIFFRACTIONr_mcbond_other0.1531.5593
X-RAY DIFFRACTIONr_mcangle_it1.57422375
X-RAY DIFFRACTIONr_scbond_it2.3153924
X-RAY DIFFRACTIONr_scangle_it3.7434.5897
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 35 -
Rwork0.274 802 -
obs--91.58 %

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