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- PDB-3i64: Crystal structure of an O-methyltransferase (NcsB1) from neocarzi... -

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Basic information

Entry
Database: PDB / ID: 3i64
TitleCrystal structure of an O-methyltransferase (NcsB1) from neocarzinostatin biosynthesis in complex with S-adenosyl-L-homocysteine (SAH) and 1,4-dihydroxy-2-naphthoic acid (DHN)
ComponentsO-methyltransferase
KeywordsTRANSFERASE / co-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
1,4-dihydroxy-2-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: 3 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 6, 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)70,6288
Polymers69,2662
Non-polymers1,3616
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-33.5 kcal/mol
Surface area24230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.031, 108.031, 211.854
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-DNA / 1,4-dihydroxy-2-naphthoic acid / 1,4-dihydroxynaphthalene-2-carboxylic acid


Mass: 204.179 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H8O4
#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.: 95 / 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: 76.13 %
Crystal growTemperature: 293 K / pH: 3.8
Details: 3.9 M Sodium formate, 10% Glycerol, 2 mM SAH, 2 mM DHN, 10 mM beta-Mercaptoethanol, pH 3.8, 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
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 14, 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: 2.98→50 Å / Num. obs: 28394 / % possible obs: 99.8 % / Redundancy: 12.6 % / Biso Wilson estimate: 80.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 29.2
Reflection shellResolution: 2.98→3.09 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

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

1tw2


Resolution: 3→50 Å / Cross valid method: FREE R
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2698 -RANDOM
Rwork0.217 ---
obs0.217 26923 96.3 %-
Displacement parametersBiso mean: 69.1 Å2
Baniso -1Baniso -2Baniso -3
1-8.48 Å220.2 Å20 Å2
2--8.48 Å20 Å2
3----16.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.39 Å
Luzzati d res low-3.2 Å
Luzzati sigma a0.33 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4812 0 94 95 5001
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.355 479 -
Rwork0.312 --
obs--89.9 %

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