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- PDB-3i58: Crystal structure of an O-methyltransferase (NcsB1) from neocarzi... -

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Basic information

Entry
Database: PDB / ID: 3i58
TitleCrystal structure of an O-methyltransferase (NcsB1) from neocarzinostatin biosynthesis in complex with S-adenosyl-L-homocysteine (SAH) and 2-hydroxy-7-methoxy-5-methyl naphthoic acid (NA)
ComponentsO-methyltransferase
KeywordsTRANSFERASE / ternary complex / Rossmann-like fold / Methyltransferase
Function / homology
Function and homology information


2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / O-methyltransferase activity / antibiotic biosynthetic process / methylation / protein dimerization activity
Similarity search - Function
Helix Hairpins - #1350 / Plant methyltransferase dimerisation / O-methyltransferase dimerisation domain / O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helix Hairpins ...Helix Hairpins - #1350 / Plant methyltransferase dimerisation / O-methyltransferase dimerisation domain / O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helix Hairpins / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2-hydroxy-7-methoxy-5-methyl naphthoic acid / S-ADENOSYL-L-HOMOCYSTEINE / 2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase
Similarity search - Component
Biological speciesStreptomyces carzinostaticus subsp. neocarzinostaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsCooke, H.A. / Bruner, S.D.
CitationJournal: Biochemistry / Year: 2009
Title: Molecular basis of substrate promiscuity for the SAM-dependent O-methyltransferase NcsB1, involved in the biosynthesis of the enediyne antitumor antibiotic neocarzinostatin.
Authors: Cooke, H.A. / Guenther, E.L. / Luo, Y. / Shen, B. / Bruner, S.D.
History
DepositionJul 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Sep 6, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: O-methyltransferase
B: O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6848
Polymers69,2662
Non-polymers1,4176
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-31.1 kcal/mol
Surface area24270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.392, 108.392, 210.321
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein O-methyltransferase


Mass: 34633.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces carzinostaticus subsp. neocarzinostaticus (bacteria)
Gene: ncsb1 / Plasmid: pBS5002 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q84HC8, Transferases; Transferring one-carbon groups; Methyltransferases
#2: 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
#3: Chemical ChemComp-7NA / 2-hydroxy-7-methoxy-5-methyl naphthoic acid / 2-hydroxy-7-methoxy-5-methylnaphthalene-1-carboxylic acid


Mass: 232.232 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H12O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 5.15 Å3/Da / Density % sol: 76.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 3.66 M Sodium formate, 10% Glycerol, 2 mM SAH, 2 mM NA, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 4, 2008
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.69→30 Å / Num. obs: 38115 / % possible obs: 98.5 % / Redundancy: 17.3 % / Biso Wilson estimate: 70.7 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 17.3
Reflection shellResolution: 2.69→2.8 Å / Redundancy: 17.8 % / Rmerge(I) obs: 0.094 / Mean I/σ(I) obs: 7 / Num. unique all: 3866

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TW2

1tw2


Resolution: 2.69→30 Å
RfactorNum. reflection% reflectionSelection details
Rfree0.247 3704 -random
Rwork0.212 ---
all0.256 ---
obs0.212 37165 96 %-
Displacement parametersBiso mean: 71.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.09 Å210.3 Å20 Å2
2--4.09 Å20 Å2
3----8.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.37 Å
Luzzati d res low-3 Å
Luzzati sigma a0.26 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 2.69→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4812 0 98 163 5073
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.006
LS refinement shellResolution: 2.69→2.86 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.363 575 -
Rwork0.324 --
obs-5345 92 %

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