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- PDB-5t6b: X-ray structure of the KijD1 C3-methyltransfeerase, converted to ... -

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Basic information

Entry
Database: PDB / ID: 5t6b
TitleX-ray structure of the KijD1 C3-methyltransfeerase, converted to monomeric form
ComponentsSugar 3-C-methyl transferase
KeywordsTRANSFERASE / 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: 2 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)187,41418
Polymers183,9354
Non-polymers3,47914
Water13,277737
1
A: Sugar 3-C-methyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9515
Polymers45,9841
Non-polymers9674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sugar 3-C-methyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9515
Polymers45,9841
Non-polymers9674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Sugar 3-C-methyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7564
Polymers45,9841
Non-polymers7723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Sugar 3-C-methyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7564
Polymers45,9841
Non-polymers7723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.707, 82.455, 82.825
Angle α, β, γ (deg.)96.05, 110.70, 112.09
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Sugar 3-C-methyl transferase


Mass: 45983.754 Da / Num. of mol.: 4
Mutation: K92M, Q95R, R96D, L97F, A105P, D388E, R398H, R412H, V413I, L414R
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 , 5 types, 751 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N2O8P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 737 / 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: 1.94 Å3/Da / Density % sol: 36.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 18-22% PEG-3350, 2%MPD, 100 mM MES, 10 mM TDP, 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: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→75 Å / Num. obs: 90291 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rsym value: 0.074 / Net I/σ(I): 7.3
Reflection shellResolution: 2→2.1 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 2.1 / % possible all: 91

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T64

5t64


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.861 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.191 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23424 4528 5 %RANDOM
Rwork0.17556 ---
obs0.17855 85763 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å2-0.11 Å20.09 Å2
2--0.45 Å20.6 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12428 0 216 737 13381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01913014
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212082
X-RAY DIFFRACTIONr_angle_refined_deg1.7731.96617699
X-RAY DIFFRACTIONr_angle_other_deg1.038327684
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.65951607
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96922.331635
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.553151955
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.32515135
X-RAY DIFFRACTIONr_chiral_restr0.0990.21935
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02114801
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023168
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_it1.8792.3786407
X-RAY DIFFRACTIONr_mcbond_other1.8792.3786406
X-RAY DIFFRACTIONr_mcangle_it2.9613.5547994
X-RAY DIFFRACTIONr_mcangle_other2.9613.5547995
X-RAY DIFFRACTIONr_scbond_it2.3892.6386607
X-RAY DIFFRACTIONr_scbond_other2.3682.6386603
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8173.8539691
X-RAY DIFFRACTIONr_long_range_B_refined5.4418.82814695
X-RAY DIFFRACTIONr_long_range_B_other5.43918.82814696
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 304 -
Rwork0.274 5988 -
obs--90.51 %

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