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- PDB-5t67: x-ray structure of the KijD1 C3-methyltransferase from Actinomadu... -

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Basic information

Entry
Database: PDB / ID: 5t67
Titlex-ray structure of the KijD1 C3-methyltransferase from Actinomadura kijaniata in complex with SAH and dTDP-sugar product
ComponentsSugar 3-C-methyl transferase
KeywordsTRANSFERASE / C3-methyltransferase / antitumor / antibiotic / kijanimicin
Function / homology
Function and homology information


transferase activity / 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 / S-ADENOSYL-L-HOMOCYSTEINE / Sugar 3-C-methyl transferase
Similarity search - Component
Biological speciesActinomadura kijaniata (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsHolden, H.M. / Thoden, J.B. / Dow, G.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)gm115921 United States
CitationJournal: Protein Sci. / Year: 2016
Title: Structural studies on KijD1, a sugar C-3'-methyltransferase.
Authors: Dow, G.T. / Thoden, J.B. / Holden, H.M.
History
DepositionSep 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Structure summary
Revision 1.3Dec 7, 2016Group: Database references
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 4, 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
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sugar 3-C-methyl transferase
B: Sugar 3-C-methyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,97815
Polymers91,6592
Non-polymers2,31913
Water14,124784
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-10 kcal/mol
Surface area29530 Å2
Unit cell
Length a, b, c (Å)51.088, 108.893, 142.783
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Sugar 3-C-methyl transferase


Mass: 45829.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinomadura kijaniata (bacteria) / Gene: KijD1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosettsa2(DE3) / References: UniProt: B3TMQ9

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Non-polymers , 7 types, 797 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: 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
#4: 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.: 2 / Source method: obtained synthetically / Formula: C17H27N3O13P2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 784 / 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: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20-23% PEG-3350, 100 mM MOPS, 100 mM MgCl2, 10 mM dTDP, 5 mM SAH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Oct 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 102095 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rsym value: 0.079 / Net I/σ(I): 9
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 2 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 2.1 / % possible all: 88.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5t64

5t64


Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.85 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.112 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24906 5084 5 %RANDOM
Rwork0.19834 ---
obs0.20081 97001 96.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.306 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å20 Å20 Å2
2--0.65 Å20 Å2
3---0.51 Å2
Refinement stepCycle: 1 / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6278 0 143 784 7205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196621
X-RAY DIFFRACTIONr_bond_other_d0.0010.026170
X-RAY DIFFRACTIONr_angle_refined_deg2.1371.9739010
X-RAY DIFFRACTIONr_angle_other_deg1.056314132
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9345820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.81422.327318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67415997
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7591569
X-RAY DIFFRACTIONr_chiral_restr0.1350.2988
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217519
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021600
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_it2.6632.0333253
X-RAY DIFFRACTIONr_mcbond_other2.6632.0333252
X-RAY DIFFRACTIONr_mcangle_it3.543.0364064
X-RAY DIFFRACTIONr_mcangle_other3.543.0354065
X-RAY DIFFRACTIONr_scbond_it3.3022.2933368
X-RAY DIFFRACTIONr_scbond_other3.3022.2933368
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6553.3374941
X-RAY DIFFRACTIONr_long_range_B_refined6.38217.1428130
X-RAY DIFFRACTIONr_long_range_B_other6.38217.1458131
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 335 -
Rwork0.345 6279 -
obs--85.81 %

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