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- PDB-8r1r: Structure of the Diels Alderase TedJ, in complex with cofactor FAD -

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Basic information

Entry
Database: PDB / ID: 8r1r
TitleStructure of the Diels Alderase TedJ, in complex with cofactor FAD
ComponentsShort-chain dehydrogenase/reductase
KeywordsOXIDOREDUCTASE / Diels Alderase / decalin cyclase / tetradecamycin / class II spirotetronate
Function / homologyAromatic-ring hydroxylase, C-terminal / : / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / FAD-binding domain / FAD binding domain / FAD binding / FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / Short-chain dehydrogenase/reductase
Function and homology information
Biological speciesStreptomyces (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsBack, C.R. / Race, P.R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T001968/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M012107/1 United Kingdom
CitationJournal: To Be Published
Title: The Diels-Alderase TedJ: Structure, Function and as a Biocatalyst for the Total Synthesis of the Antibiotic (-)-13-Deoxytetrodecamycin
Authors: Russell, J. / Back, C.R. / Perry, C. / Cheung, K. / Hayes, M.A. / van der Kamp, M.W. / Race, P.R. / Willis, C.L.
History
DepositionNov 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Short-chain dehydrogenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7982
Polymers53,0131
Non-polymers7861
Water3,081171
1
A: Short-chain dehydrogenase/reductase
hetero molecules

A: Short-chain dehydrogenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,5964
Polymers106,0252
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area4980 Å2
ΔGint-28 kcal/mol
Surface area38490 Å2
Unit cell
Length a, b, c (Å)70.250, 70.250, 203.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-681-

HOH

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Components

#1: Protein Short-chain dehydrogenase/reductase / Diels Aldrease TedJ


Mass: 53012.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Synthetic gene / Source: (gene. exp.) Streptomyces (bacteria) / Strain: WAC04657 / Gene: tedJ / Plasmid: pOPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A150VPP7
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.37 Å3/Da / Density % sol: 48.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.4 M sodium acetate trihydrate, 0.1 M sodium cacodylate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.59→101.85 Å / Num. obs: 69717 / % possible obs: 100 % / Redundancy: 25.2 % / CC1/2: 1 / Rmerge(I) obs: 0.153 / Net I/σ(I): 13.27
Reflection shellResolution: 1.59→1.62 Å / Redundancy: 21.46 % / Num. unique obs: 3433 / CC1/2: 0.385 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→66.5 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.805 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2441 3662 5.3 %RANDOM
Rwork0.20686 ---
obs0.20877 65939 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.056 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å2-0 Å2-0 Å2
2--1.25 Å2-0 Å2
3----2.5 Å2
Refinement stepCycle: 1 / Resolution: 1.59→66.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3601 0 53 171 3825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123743
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163535
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.6475124
X-RAY DIFFRACTIONr_angle_other_deg0.5141.5678099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4925490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.153539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.20610516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024528
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02847
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8233.3391966
X-RAY DIFFRACTIONr_mcbond_other2.8233.3391966
X-RAY DIFFRACTIONr_mcangle_it3.7945.9832454
X-RAY DIFFRACTIONr_mcangle_other3.7955.9852455
X-RAY DIFFRACTIONr_scbond_it4.0853.7631777
X-RAY DIFFRACTIONr_scbond_other4.0883.7651774
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1486.6892671
X-RAY DIFFRACTIONr_long_range_B_refined7.1432.314091
X-RAY DIFFRACTIONr_long_range_B_other7.14532.294068
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.59→1.631 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 274 -
Rwork0.414 4804 -
obs--100 %

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