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- PDB-4e2x: X-ray Structure of the Y222F mutant of TcaB9, a C-3'-Methyltransf... -

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Basic information

Entry
Database: PDB / ID: 4e2x
TitleX-ray Structure of the Y222F mutant of TcaB9, a C-3'-Methyltransferase, in Complex with S-Adenosyl-L-Homocysteine and dTDP
ComponentsTcaB9
KeywordsTRANSFERASE / kijanose / tetronitrose / tetradeoxy sugar / sugar methylation
Function / homology
Function and homology information


methyltransferase activity / methylation / metal ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3100 / Methyltransferase, zinc-binding domain / Methyltransferase putative zinc binding domain / C-methyltransferase / Methyltransferase putative zinc binding domain superfamily / Putative zinc binding domain / C-methyltransferase C-terminal domain / Methyltransferase domain / N-terminal domain of TfIIb / Other non-globular ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3100 / Methyltransferase, zinc-binding domain / Methyltransferase putative zinc binding domain / C-methyltransferase / Methyltransferase putative zinc binding domain superfamily / Putative zinc binding domain / C-methyltransferase C-terminal domain / Methyltransferase domain / N-terminal domain of TfIIb / Other non-globular / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Vaccinia Virus protein VP39 / Helix non-globular / Special / NAD(P)-binding Rossmann-like Domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / THYMIDINE-5'-DIPHOSPHATE / Methyltransferase
Similarity search - Component
Biological speciesMicromonospora chalcea (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBruender, N.A. / Holden, H.M.
CitationJournal: Protein Sci. / Year: 2012
Title: Probing the catalytic mechanism of a C-3'-methyltransferase involved in the biosynthesis of D-tetronitrose.
Authors: Bruender, N.A. / Holden, H.M.
History
DepositionMar 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _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: TcaB9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1758
Polymers46,0751
Non-polymers1,1007
Water8,521473
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.542, 114.174, 37.632
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-825-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein TcaB9 / C-3'-Methyltransferase


Mass: 46074.914 Da / Num. of mol.: 1 / Mutation: Y222F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora chalcea (bacteria) / Gene: tcab9 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 DE3
References: UniProt: B5L6K6, Transferases; Transferring one-carbon groups; Methyltransferases

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Non-polymers , 5 types, 480 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 2.34 Å3/Da / Density % sol: 47.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.2-1.6 M sodium/potassium phosphate, 10 mM dTMP, 5 mM S-adenosyl-L-homocysteine, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: May 12, 2011 / Details: Montel
RadiationMonochromator: nickel filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.4→38 Å / Num. all: 86374 / Num. obs: 81798 / % possible obs: 94.7 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 10.3
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 1.74 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1.83 / Num. unique all: 13540 / Rsym value: 0.34 / % possible all: 85.2

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
REFMAC5.5.0109refinement
SAINTdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NDJ

3ndj


Resolution: 1.4→38 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.54 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23641 4112 5 %RANDOM
Rwork0.20447 ---
obs0.20607 77644 94.74 %-
all-81756 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.959 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20 Å2
2--0.19 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.4→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3161 0 68 473 3702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223324
X-RAY DIFFRACTIONr_angle_refined_deg2.2671.9744516
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6525412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55423.043161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29515518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1441531
X-RAY DIFFRACTIONr_chiral_restr0.1680.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212575
X-RAY DIFFRACTIONr_mcbond_it1.9621.52033
X-RAY DIFFRACTIONr_mcangle_it2.85323275
X-RAY DIFFRACTIONr_scbond_it4.37531291
X-RAY DIFFRACTIONr_scangle_it6.8754.51237
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 263 -
Rwork0.406 4890 -
obs--81.92 %

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