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- PDB-8rqh: Crystal Structure of the flavoprotein monooxygenase TrlE from Str... -

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Basic information

Entry
Database: PDB / ID: 8rqh
TitleCrystal Structure of the flavoprotein monooxygenase TrlE from Streptomyces cyaneofuscatus Soc7
ComponentsTropone 2-monooxygenase
KeywordsFLAVOPROTEIN / tropolone / fad / oxidoreductase / decarboxylation
Function / homology: / FAD-binding domain / FAD binding domain / FAD binding / monooxygenase activity / FAD/NAD(P)-binding domain superfamily / membrane / FLAVIN-ADENINE DINUCLEOTIDE / Tropone 2-monooxygenase
Function and homology information
Biological speciesStreptomyces cyaneofuscatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSowa, S.T. / Hoeing, L.S. / Jakob, R.P. / Maier, T. / Teufel, R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation212747 Switzerland
CitationJournal: Chem Sci / Year: 2024
Title: Biosynthesis of the bacterial antibiotic 3,7-dihydroxytropolone through enzymatic salvaging of catabolic shunt products.
Authors: Hoing, L. / Sowa, S.T. / Toplak, M. / Reinhardt, J.K. / Jakob, R. / Maier, T. / Lill, M.A. / Teufel, R.
History
DepositionJan 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tropone 2-monooxygenase
B: Tropone 2-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3089
Polymers92,3782
Non-polymers1,9307
Water2,846158
1
A: Tropone 2-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1064
Polymers46,1891
Non-polymers9173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tropone 2-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2025
Polymers46,1891
Non-polymers1,0134
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.900, 112.900, 148.570
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: PRO / End label comp-ID: PRO / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 4 - 394 / Label seq-ID: 30 - 420

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Tropone 2-monooxygenase


Mass: 46189.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cyaneofuscatus (bacteria) / Gene: trlE / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S1JZI9
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.96 Å3/Da / Density % sol: 58.43 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M BIS-TRIS propane pH 8.5 0.25 M Na2SO4 15% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 38458 / % possible obs: 99.93 % / Redundancy: 20.6 % / CC1/2: 0.999 / Net I/σ(I): 14.02
Reflection shellResolution: 2.5→2.589 Å / Num. unique obs: 3789 / CC1/2: 0.554

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→49.572 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 9.947 / SU ML: 0.206 / Cross valid method: FREE R-VALUE / ESU R: 0.342 / ESU R Free: 0.247
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2385 1923 5.001 %
Rwork0.1912 36529 -
all0.194 --
obs-38452 99.964 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 64.575 Å2
Baniso -1Baniso -2Baniso -3
1-0.036 Å20.018 Å20 Å2
2--0.036 Å2-0 Å2
3----0.118 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5761 0 123 158 6042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0126051
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165612
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.6618254
X-RAY DIFFRACTIONr_angle_other_deg0.4511.58712793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9295763
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.012575
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.667202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.32110854
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.310277
X-RAY DIFFRACTIONr_chiral_restr0.060.2885
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027569
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021513
X-RAY DIFFRACTIONr_nbd_refined0.2020.21130
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.25060
X-RAY DIFFRACTIONr_nbtor_refined0.1760.22869
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.23294
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2166
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0060.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1390.218
X-RAY DIFFRACTIONr_nbd_other0.1820.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1670.29
X-RAY DIFFRACTIONr_mcbond_it5.7736.4883058
X-RAY DIFFRACTIONr_mcbond_other5.7566.4883058
X-RAY DIFFRACTIONr_mcangle_it8.1511.6513819
X-RAY DIFFRACTIONr_mcangle_other8.14911.6533820
X-RAY DIFFRACTIONr_scbond_it6.2736.9692993
X-RAY DIFFRACTIONr_scbond_other6.2116.9532978
X-RAY DIFFRACTIONr_scangle_it8.99412.5354435
X-RAY DIFFRACTIONr_scangle_other8.90912.5084418
X-RAY DIFFRACTIONr_lrange_it10.85563.2346452
X-RAY DIFFRACTIONr_lrange_other10.85363.2486445
X-RAY DIFFRACTIONr_ncsr_local_group_10.0790.0511684
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.079440.05009
12AX-RAY DIFFRACTIONLocal ncs0.079440.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.5-2.5650.4431410.40626890.40828310.8960.90399.96470.404
2.565-2.6350.3871350.34725620.34926990.9110.93699.92590.328
2.635-2.7110.4071330.3125260.31526600.9110.94899.96240.287
2.711-2.7940.3281300.28124610.28425910.9430.9571000.252
2.794-2.8860.3321250.25423740.25824990.9310.9621000.223
2.886-2.9870.2821210.20623090.20924300.9610.9751000.178
2.987-3.0990.271170.19722120.223290.9640.9781000.168
3.099-3.2250.2271130.1921610.19222750.9660.9899.9560.169
3.225-3.3680.3131090.20720550.21221640.9430.9751000.189
3.368-3.5310.2291040.19919820.20120860.9640.9791000.184
3.531-3.7210.231980.18418660.18619640.9690.9831000.173
3.721-3.9450.214940.1717820.17218760.9750.9861000.161
3.945-4.2160.179890.15316950.15417840.9840.9881000.146
4.216-4.5510.192830.15515840.15716670.9780.9861000.149
4.551-4.9810.185760.14414430.14615200.9780.98799.93420.14
4.981-5.5620.264700.17413270.17813970.9670.9841000.169
5.562-6.4090.275620.18311790.18712410.9710.9831000.175
6.409-7.8170.211540.16810130.1710670.9770.9861000.17
7.817-10.920.164420.158100.158520.9820.9871000.16
10.92-49.5720.202270.2464990.2445270.9790.96299.81020.27

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