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- PDB-1n5v: Crystal structure of a Monooxygenase from the gene ActVA-Orf6 of ... -

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Basic information

Entry
Database: PDB / ID: 1n5v
TitleCrystal structure of a Monooxygenase from the gene ActVA-Orf6 of Streptomyces coelicolor in complex with the ligand Nanaomycin D
ComponentsActVA-Orf6 monooxygenase
KeywordsOXIDOREDUCTASE / monooxygenase / aromatic polyketides / actinorhodin / dihydrokalafungin / nanaomycin D / streptomyces coelicolor
Function / homology
Function and homology information


ABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NOM / ActVA 6 protein
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / fourier difference / Resolution: 2.24 Å
AuthorsSciara, G. / Kendrew, S.G. / Miele, A.E. / Marsh, N.G. / Federici, L. / Malatesta, F. / Schimperna, G. / Savino, C. / Vallone, B.
Citation
Journal: Embo J. / Year: 2003
Title: The structure of ActVA-Orf6, a novel type of monooxygenase involved in actinorhodin biosynthesis
Authors: Sciara, G. / Kendrew, S.G. / Miele, A.E. / Marsh, N.G. / Federici, L. / Malatesta, F. / Schimperna, G. / Savino, C. / Vallone, B.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and preliminary X-ray diffraction studies of a monooxygenase from Streptomyces coelicolor A3(2) involved in the biosynthesis of the polyketide actinorhodin
Authors: Kendrew, S.G. / Federici, L. / Savino, C. / Miele, A.E. / Marsh, E.N. / Vallone, B.
#2: Journal: J.Bacteriol. / Year: 1997
Title: Identification of a monooxygenase from Streptomyces coelicolor A3 (2) involved in the biosynthesis of actinorhodin: purification and characterization of the recombinant enzyme
Authors: Kendrew, S.G. / Hopwood, D.A. / Marsh, E.N.
History
DepositionNov 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: 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: ActVA-Orf6 monooxygenase
B: ActVA-Orf6 monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2573
Polymers23,9572
Non-polymers3001
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-26 kcal/mol
Surface area10410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.389, 59.921, 71.597
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a dimer in the asymmetric unit

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Components

#1: Protein ActVA-Orf6 monooxygenase


Mass: 11978.420 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: ActVA-Orf6 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53908
#2: Chemical ChemComp-NOM / 7-HYDROXY-5-METHYL-3,3A,5,11B-TETRAHYDRO-1,4-DIOXA-CYCLOPENTA[A]ANTHRACENE-2,6,11-TRIONE / NANAOMYCIN D


Mass: 300.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.04 Å3/Da / Density % sol: 39.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion cocrystals / pH: 7
Details: ammonium sulfate, PEG 200, Tris or Hepes buffer , pH 7.0, vapour diffusion cocrystals, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.5 Mammonium sulfate1reservoir
2100 mMHEPES1reservoirpH7.0
3100 mMTris-HCl1reservoirpH8.0
410-15 %PEG2001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 26, 2001 / Details: Three-segment Pt-coated toroidal mirror
RadiationMonochromator: Double crystal (Si111,Si220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.24→20 Å / Num. all: 10268 / Num. obs: 10268 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 29.23 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 12.4
Reflection shellResolution: 2.24→2.28 Å / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 2.1 / Num. unique all: 485 / % possible all: 99
Reflection
*PLUS
Num. measured all: 68040
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
RefinementMethod to determine structure: fourier difference
Starting model: PDB ENTRY 1LQ9

1lq9


Resolution: 2.24→20 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 493 -RANDOM
Rwork0.214 ---
all-10232 --
obs-10232 99.5 %-
Refinement stepCycle: LAST / Resolution: 2.24→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1692 0 22 60 1774
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.013
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg2.8

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