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- PDB-2res: Tetracenomycin ARO/CYC mutant R69A -

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Basic information

Entry
Database: PDB / ID: 2res
TitleTetracenomycin ARO/CYC mutant R69A
ComponentsMultifunctional cyclase-dehydratase-3-O-methyl transferase tcmN
KeywordsBIOSYNTHETIC PROTEIN / TETRACENOMYCIN / POLYKETIDE / AROMATASE / CYCLASE / DEHYDRATASE / HELIX-GRIP / Antibiotic biosynthesis / Methyltransferase / Multifunctional enzyme / Transferase / LYASE
Function / homology
Function and homology information


tetracenomycin F2 synthase / O-methyltransferase activity / antibiotic biosynthetic process / Transferases; Transferring one-carbon groups; Methyltransferases / methylation
Similarity search - Function
Coenzyme Q-binding protein COQ10, START domain / Polyketide cyclase / dehydrase and lipid transport / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / Winged helix DNA-binding domain superfamily ...Coenzyme Q-binding protein COQ10, START domain / Polyketide cyclase / dehydrase and lipid transport / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tetracenomycin biosynthesis bifunctional cyclase/O-methyl transferase TcmN
Similarity search - Component
Biological speciesStreptomyces glaucescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAmes, B.D. / Tsai, S.C.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Crystal structure and functional analysis of tetracenomycin ARO/CYC: implications for cyclization specificity of aromatic polyketides.
Authors: Ames, B.D. / Korman, T.P. / Zhang, W. / Smith, P. / Vu, T. / Tang, Y. / Tsai, S.C.
History
DepositionSep 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Multifunctional cyclase-dehydratase-3-O-methyl transferase tcmN


Theoretical massNumber of molelcules
Total (without water)19,8521
Polymers19,8521
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.080, 105.080, 51.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Multifunctional cyclase-dehydratase-3-O-methyl transferase tcmN / TETRACENOMYCIN C AROMATASE/CYCLASE


Mass: 19852.229 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN / Mutation: R69A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces glaucescens (bacteria) / Gene: tcmN / Plasmid: PET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P16559
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 21% PEG 8000, 0.1M SODIUM ACETATE, pH 4.60, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 12, 2005 / Details: MIRRORS
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 2.2→50 Å / Num. all: 10209 / Num. obs: 9992 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 18.6 Å2 / Rsym value: 0.072 / Net I/σ(I): 24.7
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 436 / Rsym value: 0.438 / % possible all: 83.2

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→38.91 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1519 -RANDOM
Rwork0.21 ---
all-10333 --
obs-9673 93.6 %-
Displacement parametersBiso mean: 31 Å2
Baniso -1Baniso -2Baniso -3
1--3.23 Å2--
2--7.23 Å2-
3----4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→38.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1239 0 0 75 1314
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.023
RfactorNum. reflection% reflection
Rfree0.317 188 -
Rwork0.268 --
obs--81.5 %

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