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- PDB-2rez: Tetracenomycin ARO/CYC NaI Structure -

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Basic information

Entry
Database: PDB / ID: 2rez
TitleTetracenomycin ARO/CYC NaI Structure
ComponentsMultifunctional cyclase-dehydratase-3-O-methyl transferase tcmN
KeywordsBIOSYNTHETIC PROTEIN / TETRACENOMYCIN / POLYKETIDE / AROMATASE / CYCLASE / DEHYDRATASE / HELIX-GRIP / DOUBLE-HOT-DOG / 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
ACETATE ION / IODIDE ION / Tetracenomycin biosynthesis bifunctional cyclase/O-methyl transferase TcmN
Similarity search - Component
Biological speciesStreptomyces glaucescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Multifunctional cyclase-dehydratase-3-O-methyl transferase tcmN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9788
Polymers18,2251
Non-polymers7537
Water2,270126
1
A: Multifunctional cyclase-dehydratase-3-O-methyl transferase tcmN
hetero molecules

A: Multifunctional cyclase-dehydratase-3-O-methyl transferase tcmN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,95616
Polymers36,4512
Non-polymers1,50514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.788, 73.788, 101.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Multifunctional cyclase-dehydratase-3-O-methyl transferase tcmN


Mass: 18225.330 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: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.78 Å3/Da / Density % sol: 67.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 20% PEG 8000, 0.1M SODIUM ACETATE, 0.1 M SODIUM IODIDE, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-3 / Wavelength: 0.97354 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 28, 2006 / Details: Mirror
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97354 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 21122 / Num. obs: 21102 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Biso Wilson estimate: 15.6 Å2 / Rsym value: 0.082 / Net I/σ(I): 25.9
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 5.6 / Num. unique all: 2074 / Rsym value: 0.49 / % possible all: 99.8

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RER

2rer


Resolution: 1.95→36.9 Å / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 3109 -Random
Rwork0.206 ---
all-21022 --
obs-20297 96.6 %-
Displacement parametersBiso mean: 27.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.2 Å2--
2---3.2 Å2-
3---6.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.95→36.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1266 0 13 126 1405
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.26 497 -
Rwork0.229 --
obs--94.1 %

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