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- PDB-1lq9: Crystal Structure of a Monooxygenase from the Gene ActVA-Orf6 of ... -

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Basic information

Entry
Database: PDB / ID: 1lq9
TitleCrystal Structure of a Monooxygenase from the Gene ActVA-Orf6 of Streptomyces coelicolor Strain A3(2)
ComponentsACTVA-ORF6 MONOOXYGENASE
KeywordsOXIDOREDUCTASE / MONOOXYGENASE / AROMATIC POLYKETIDES / ACTINORHODIN / DIHYDROKALAFUNGIN / STREPTOMYCES COELICOLOR
Function / homologyABM 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 / ActVA 6 protein
Function and homology information
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.3 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.G. / Vallone, B.
#2: Journal: J.Bacteriol. / Year: 1997
Title: Identification of a monooxygenase from Streptomyces coelicolor A3(2) involved in biosynthesis of Actinorhodin: purification and characterization of the recombinant enzyme
Authors: Kendrew, S.G. / Hopwood, D.A. / Marsh, E.N.G.
History
DepositionMay 9, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)24,1513
Polymers23,9572
Non-polymers1941
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-23 kcal/mol
Surface area11040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.028, 60.168, 71.379
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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: ammonium sulfate, PEG 200, Tris or Hepes buffer, pH 7.0, VAPOR DIFFUSION, 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: ESRF / Beamline: ID14-1 / Wavelength: 0.9326 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 4, 2000
RadiationMonochromator: DIAMOND 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9326 Å / Relative weight: 1
ReflectionResolution: 1.3→20 Å / Num. all: 50305 / Num. obs: 50305 / % possible obs: 99.7 % / Observed criterion σ(F): -4 / Redundancy: 15.9 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.059
Reflection shellResolution: 1.3→1.32 Å / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 12.2 / % possible all: 100
Reflection
*PLUS
Num. obs: 50368 / % possible obs: 99.8 % / Num. measured all: 798091
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
REFMACrefinement
RefinementMethod to determine structure: MIRAS / Resolution: 1.3→20 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.168 2560 RANDOM
Rwork0.142 --
all-50305 -
obs-50305 -
Refinement stepCycle: LAST / Resolution: 1.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1692 0 13 258 1963
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_deg0.99

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