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- PDB-2rer: Crystal structure of the aromatase/cyclase domain of TcmN from St... -

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Basic information

Entry
Database: PDB / ID: 2rer
TitleCrystal structure of the aromatase/cyclase domain of TcmN from Streptomyces glaucescens
ComponentsMultifunctional cyclase-dehydratase-3-O-methyl transferase tcmN
KeywordsBIOSYNTHETIC PROTEIN / CYCLASE / AROMATASE / POLYKETIDE / HELIX-GRIP / DEHYDRATASE / ANTICANCER / ANTIBIOTIC / Antibiotic biosynthesis / Methyltransferase / Multifunctional enzyme / Transferase
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 / MAD / Resolution: 1.9 Å
AuthorsAmes, B.D. / Korman, T.P. / Vu, T.N. / 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 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)19,9381
Polymers19,9381
Non-polymers00
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.660, 105.126, 50.259
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


Mass: 19938.344 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN
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.: 144 / 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: 2.3 Å3/Da / Density % sol: 46.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 24% PEG 8000, 0.1M SODIUM ACETATE, pH 4.60, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.210.97957
SYNCHROTRONALS 5.0.220.97956, 0.97958, 0.95372
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDDec 4, 2004MIRRORS
ADSC QUANTUM 3152CCDDec 4, 2004MIRRORS
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double-crystal, Si(111)SINGLE WAVELENGTHMx-ray1
2Double-crystal, Si(111)MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979571
20.979561
30.979581
40.953721
ReflectionResolution: 1.9→50 Å / Num. all: 15011 / Num. obs: 14977 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 20.3 Å2 / Rsym value: 0.092 / Net I/σ(I): 16.9
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 990 / Rsym value: 0.399 / % possible all: 98.2

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→31.31 Å / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1486 -MAXIMUM LIKELYHOOD
Rwork0.215 ---
all-14933 --
obs-14563 97.5 %-
Displacement parametersBiso mean: 35.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20 Å2
2---2.59 Å20 Å2
3---3.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.9→31.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1270 0 0 144 1414
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.7
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.022
RfactorNum. reflection% reflection
Rfree0.346 247 -
Rwork0.272 --
obs-2018 92.1 %

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