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- PDB-5zw3: Crystal Structure of TrmR from B. subtilis -

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Basic information

Entry
Database: PDB / ID: 5zw3
TitleCrystal Structure of TrmR from B. subtilis
ComponentsPutative O-methyltransferase YrrM
KeywordsRNA BINDING PROTEIN / transferase
Function / homology
Function and homology information


tRNA (uridine) methyltransferase activity / O-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / magnesium ion binding
Similarity search - Function
tRNA 5-hydroxyuridine methyltransferase / O-methyltransferase / Class I-like SAM-dependent O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / tRNA 5-hydroxyuridine methyltransferase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsKim, J. / Ryu, H. / Almo, S.C.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)2016R1D1A1B03930716 Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Identification of a novel tRNA wobble uridine modifying activity in the biosynthesis of 5-methoxyuridine.
Authors: Ryu, H. / Grove, T.L. / Almo, S.C. / Kim, J.
History
DepositionMay 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _entity.formula_weight
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative O-methyltransferase YrrM
B: Putative O-methyltransferase YrrM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9016
Polymers52,0842
Non-polymers8174
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-45 kcal/mol
Surface area17230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.874, 116.738, 43.437
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 3 - 217 / Label seq-ID: 3 - 217

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Putative O-methyltransferase YrrM


Mass: 26041.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: yrrM, BSU27360 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O32036, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAH / 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 1.95 Å3/Da / Density % sol: 36.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.1 M Ammonium tartrate dibasic (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 18494 / % possible obs: 99.2 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.04 / Rrim(I) all: 0.1 / Χ2: 1.463 / Net I/σ(I): 8.4 / Num. measured all: 113363
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.27-2.315.10.4138780.9760.2020.4621.29697.6
2.31-2.356.10.399060.970.1720.4281.391100
2.35-2.46.30.359280.9810.1510.3821.373100
2.4-2.456.30.3529090.9870.1540.3851.408100
2.45-2.56.30.3229040.9850.1390.3521.402100
2.5-2.566.30.2549270.9870.110.2781.4100
2.56-2.626.40.2568870.9890.1110.281.513100
2.62-2.696.30.2429420.9890.1060.2651.55299.8
2.69-2.776.30.1999070.990.0860.2181.452100
2.77-2.866.30.189280.9910.0780.1971.54100
2.86-2.966.30.1469160.9940.0640.161.503100
2.96-3.086.30.1329280.9950.0570.1441.568100
3.08-3.226.30.1029220.9960.0440.1111.52100
3.22-3.396.20.0889350.9960.0390.0971.494100
3.39-3.66.20.0779320.9970.0340.0841.5399.8
3.6-3.886.10.0729410.9980.0320.0791.68999.6
3.88-4.276.10.0639380.9970.0270.0681.59399.9
4.27-4.8960.0569540.9980.0250.0621.42699.8
4.89-6.165.90.0589630.9970.0260.0641.23599
6.16-505.50.069490.9970.0280.0671.29890.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GPY

2gpy


Resolution: 2.27→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.932 / SU B: 11.195 / SU ML: 0.246 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.442 / ESU R Free: 0.269
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2661 899 4.9 %RANDOM
Rwork0.213 ---
obs0.2156 17560 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 115.74 Å2 / Biso mean: 46.317 Å2 / Biso min: 26.31 Å2
Baniso -1Baniso -2Baniso -3
1-6.53 Å20 Å20 Å2
2---5.96 Å20 Å2
3----0.57 Å2
Refinement stepCycle: final / Resolution: 2.27→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3204 0 54 88 3346
Biso mean--34.43 43.11 -
Num. residues----400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.0193331
X-RAY DIFFRACTIONr_bond_other_d00.023048
X-RAY DIFFRACTIONr_angle_refined_deg0.4151.9794526
X-RAY DIFFRACTIONr_angle_other_deg0.45237076
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9855396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15125.061164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15915555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9381514
X-RAY DIFFRACTIONr_chiral_restr0.0340.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0213656
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02634
Refine LS restraints NCS

Ens-ID: 1 / Number: 12434 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.273→2.332 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 67 -
Rwork0.353 1162 -
all-1229 -
obs--91.92 %

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