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- PDB-3ndj: X-ray Structure of a C-3'-Methyltransferase in Complex with S-Ade... -

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Basic information

Entry
Database: PDB / ID: 3ndj
TitleX-ray Structure of a C-3'-Methyltransferase in Complex with S-Adenosyl-L-Homocysteine and Sugar Product
ComponentsMethyltransferase
KeywordsTRANSFERASE / S-adenosyl-L-homocysteine / kijanose / tetronitrose / tetradeoxy sugar / keto sugar / Micromonospora chalcea / TcaB9 / C-3'-Methyltransferase / 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
Chem-JHZ / PHOSPHATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase
Similarity search - Component
Biological speciesMicromonospora chalcea (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBruender, N.A. / Thoden, J.B. / Kaur, M. / Avey, M.K. / Holden, H.M.
CitationJournal: Biochemistry / Year: 2010
Title: Molecular Architecture of a C-3'-Methyltransferase Involved in the Biosynthesis of d-Tetronitrose.
Authors: Bruender, N.A. / Thoden, J.B. / Kaur, M. / Avey, M.K. / Holden, H.M.
History
DepositionJun 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 23, 2012Group: Atomic model
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1795
Polymers46,0911
Non-polymers1,0884
Water7,350408
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.944, 114.447, 37.825
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-580-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Methyltransferase /


Mass: 46090.914 Da / Num. of mol.: 1
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

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Non-polymers , 5 types, 412 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-JHZ / (2R,4S,6R)-4-amino-4,6-dimethyl-5-oxotetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)


Mass: 543.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O13P2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.37 Å3/Da / Density % sol: 48.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.3 M - 1.5 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: Apr 6, 2010 / 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→57.2 Å / Num. all: 87047 / Num. obs: 84778 / % possible obs: 97.4 % / Redundancy: 4.21 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 11.09
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 2.42 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 2.6 / Num. unique all: 14813 / Rsym value: 0.254 / % possible all: 94

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
REFMAC5.5.0066refinement
SAINTdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: In-house MIR model

Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.91 / SU B: 1.596 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23973 3476 5 %RANDOM
Rwork0.20314 ---
all0.205 69883 --
obs0.20499 66407 98.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2--0.15 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3162 0 67 408 3637
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223359
X-RAY DIFFRACTIONr_angle_refined_deg2.2221.9774582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2125420
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23623.054167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03615524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0171533
X-RAY DIFFRACTIONr_chiral_restr0.1520.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212622
X-RAY DIFFRACTIONr_mcbond_it1.6561.52045
X-RAY DIFFRACTIONr_mcangle_it2.32123298
X-RAY DIFFRACTIONr_scbond_it3.49331314
X-RAY DIFFRACTIONr_scangle_it4.994.51276
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 250 -
Rwork0.275 4681 -
obs--95.69 %

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