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- PDB-4k5s: The crystal structure of premithramycin B in complex with MTMOIV,... -

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Basic information

Entry
Database: PDB / ID: 4k5s
TitleThe crystal structure of premithramycin B in complex with MTMOIV, a baeyer-villiger monooxygenase from the mithramycin biosynthetic pathway in streptomyces argillaceus.
ComponentsOxygenase
KeywordsOXIDOREDUCTASE / OXYGENASE / MITHRAMYCIN / BAEYER-VILLIGER / FLAVIN BINDING PROTEIN / ROSSMANN FOLD / FAD BINDING PROTEIN
Function / homology
Function and homology information


Alpha-Beta Plaits - #2450 / Aromatic-ring hydroxylase, C-terminal / Glutaredoxin - #120 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / Glutaredoxin / FAD/NAD(P)-binding domain superfamily ...Alpha-Beta Plaits - #2450 / Aromatic-ring hydroxylase, C-terminal / Glutaredoxin - #120 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / Glutaredoxin / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / premithramycin B / Oxygenase
Similarity search - Component
Biological speciesStreptomyces argillaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNoinaj, N. / Bosserman, M.A. / Rohr, J. / Buchanan, S.K.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Molecular Insight into Substrate Recognition and Catalysis of Baeyer-Villiger Monooxygenase MtmOIV, the Key Frame-Modifying Enzyme in the Biosynthesis of Anticancer Agent Mithramycin.
Authors: Bosserman, M.A. / Downey, T. / Noinaj, N. / Buchanan, S.K. / Rohr, J.
History
DepositionApr 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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: Oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1883
Polymers57,3101
Non-polymers1,8792
Water9,152508
1
A: Oxygenase
hetero molecules

A: Oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,3776
Polymers114,6192
Non-polymers3,7574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5210 Å2
ΔGint-28 kcal/mol
Surface area38190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.715, 79.748, 154.264
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-895-

HOH

21A-919-

HOH

31A-1006-

HOH

41A-1109-

HOH

51A-1201-

HOH

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Components

#1: Protein Oxygenase /


Mass: 57309.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces argillaceus (bacteria) / Gene: mtmOIV / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q194P4
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-PM0 / premithramycin B / (1S,4aS,12aS)-3-acetyl-9-{[2,6-dideoxy-3-O-(2,6-dideoxy-beta-D-arabino-hexopyranosyl)-beta-D-arabino-hexopyranosyl]oxy} -2,6,7-trihydroxy-1-methoxy-8-methyl-4,5-dioxo-1,5,12,12a-tetrahydrotetracen-4a(4H)-yl 2,6-dideoxy-3-C-methyl-beta-D-ribo-hexopyranosyl-(1->3)-2,6-dideoxy-beta-D-lyxo-hexopyranosyl-(1->3)-2,6-dideoxy-beta-D- arabino-hexopyranoside


Mass: 1093.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C53H72O24
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 508 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHESE CONFLICTS REPRESENT NATURAL VARIANTS

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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: 2.99 Å3/Da / Density % sol: 58.86 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 200 mM ammonium acetate, 30% PEG 1000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 9, 2009
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→45.68 Å / Num. obs: 51450 / % possible obs: 96.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Rsym value: 0.09 / Net I/σ(I): 15.1
Reflection shellResolution: 1.9→1.92 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.71 / % possible all: 91.5

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(PHENIX.REFINE: DEV_501)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.94 Å / SU ML: 0.22 / σ(F): 1.4 / Phase error: 19.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2613 5.08 %random
Rwork0.18 ---
obs0.182 51450 93.4 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.28 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.6563 Å2-0 Å2-0 Å2
2---8.0372 Å2-0 Å2
3----8.2214 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3696 0 130 508 4334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073962
X-RAY DIFFRACTIONf_angle_d1.1395436
X-RAY DIFFRACTIONf_dihedral_angle_d21.3791520
X-RAY DIFFRACTIONf_chiral_restr0.078619
X-RAY DIFFRACTIONf_plane_restr0.004700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96730.35652280.29274303X-RAY DIFFRACTION84
1.9673-2.04590.28262720.24824346X-RAY DIFFRACTION85
2.0459-2.1390.26822310.21744485X-RAY DIFFRACTION87
2.139-2.25160.24532610.20054667X-RAY DIFFRACTION91
2.2516-2.39240.23372440.18574863X-RAY DIFFRACTION94
2.3924-2.57680.22312850.17725008X-RAY DIFFRACTION97
2.5768-2.83550.20432820.16875114X-RAY DIFFRACTION98
2.8355-3.24420.21582610.17285236X-RAY DIFFRACTION99
3.2442-4.08160.18382670.1535298X-RAY DIFFRACTION100
4.0816-19.940.17522820.14065517X-RAY DIFFRACTION100

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