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- PDB-5t64: X-ray structure of the C3-methyltransferase KijD1 from Actinomadu... -

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Basic information

Entry
Database: PDB / ID: 5t64
TitleX-ray structure of the C3-methyltransferase KijD1 from Actinomadura kijaniata in complex with TDP and SAH
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
S-ADENOSYL-L-HOMOCYSTEINE / THYMIDINE-5'-PHOSPHATE / Sugar 3-C-methyl transferase
Similarity search - Component
Biological speciesActinomadura kijaniata (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.2Dec 7, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 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)93,40013
Polymers91,6592
Non-polymers1,74111
Water12,376687
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-15 kcal/mol
Surface area30760 Å2
Unit cell
Length a, b, c (Å)51.340, 110.894, 143.251
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): Rosetta2(DE3) / References: UniProt: B3TMQ9

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Non-polymers , 6 types, 698 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N2O8P
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 687 / 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: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20-23% PEG-3350, 100 mM MgCl2, 100 mM MOPS, 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 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→87.69 Å / Num. obs: 89296 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rsym value: 0.075 / Net I/σ(I): 10.7
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 2.5 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NDI

3ndi


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.735 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.111 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22042 4471 5 %RANDOM
Rwork0.18072 ---
obs0.18273 84825 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.704 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6227 0 107 687 7021
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196551
X-RAY DIFFRACTIONr_bond_other_d0.0010.026121
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.9688911
X-RAY DIFFRACTIONr_angle_other_deg0.892314022
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3995820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.07722.312320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.368151000
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.641572
X-RAY DIFFRACTIONr_chiral_restr0.1120.2979
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217477
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021589
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_it2.2581.9643235
X-RAY DIFFRACTIONr_mcbond_other2.2571.9643234
X-RAY DIFFRACTIONr_mcangle_it3.1492.9314040
X-RAY DIFFRACTIONr_mcangle_other3.1492.9314041
X-RAY DIFFRACTIONr_scbond_it3.0742.2753316
X-RAY DIFFRACTIONr_scbond_other3.0622.2723312
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5833.2954856
X-RAY DIFFRACTIONr_long_range_B_refined6.14616.5667891
X-RAY DIFFRACTIONr_long_range_B_other6.1516.5697892
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 296 -
Rwork0.289 5842 -
obs--92.62 %

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