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- PDB-8xhy: The complex structure of mutant T307A of SsBcmE and its natural s... -

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Basic information

Entry
Database: PDB / ID: 8xhy
TitleThe complex structure of mutant T307A of SsBcmE and its natural substrate cIL
ComponentsFe/2OG dependent dioxygenase
KeywordsOXIDOREDUCTASE / C-H activation / selectivity / Fe/2OG dependent dioxygenase
Function / homology: / 2-OXOGLUTARIC ACID / :
Function and homology information
Biological speciesStreptomyces cinnamoneus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71001968611 Å
AuthorsWu, L. / Tang, G.L. / Zhou, J.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Three distinct strategies lead to programmable aliphatic C-H oxidation in bicyclomycin biosynthesis.
Authors: Wu, L. / He, J.B. / Wei, W. / Pan, H.X. / Wang, X. / Yang, S. / Liang, Y. / Tang, G.L. / Zhou, J.
History
DepositionDec 18, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fe/2OG dependent dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9016
Polymers36,2881
Non-polymers6125
Water6,972387
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.320, 81.970, 82.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Fe/2OG dependent dioxygenase


Mass: 36288.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cinnamoneus (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 392 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A1LVH / (3~{S},6~{S})-3-[(2~{S})-butan-2-yl]-6-(2-methylpropyl)piperazine-2,5-dione


Mass: 226.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H22N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.26 M Sodium phosphate monobasic monohydrate/ 0.14 M Potassium phosphate dibasic pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.71→23.70096122 Å / Num. obs: 35306 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 17.6447735935 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Net I/σ(I): 12.9
Reflection shellResolution: 1.71→1.77 Å / Redundancy: 12.9 % / Rmerge(I) obs: 1.414 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2574 / CC1/2: 0.851 / Rpim(I) all: 0.406 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSVersion June 30, 2023data reduction
XDSVersion June 30, 2023data scaling
PHASER1.12_2829phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8XHP

8xhp


Resolution: 1.71001968611→23.7009612187 Å / SU ML: 0.167067202394 / Cross valid method: FREE R-VALUE / σ(F): 1.34365123938 / Phase error: 21.2086821137
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.204977870504 1727 4.9017938238 %
Rwork0.160470432844 33505 -
obs0.162689693312 35232 99.9177561612 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.7428394878 Å2
Refinement stepCycle: LAST / Resolution: 1.71001968611→23.7009612187 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2431 0 39 387 2857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01263470502622539
X-RAY DIFFRACTIONf_angle_d1.162358869863445
X-RAY DIFFRACTIONf_chiral_restr0.0764971071442350
X-RAY DIFFRACTIONf_plane_restr0.00758645879829469
X-RAY DIFFRACTIONf_dihedral_angle_d20.91431477741475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71002-1.76030.2900255313421220.2269288485822772X-RAY DIFFRACTION99.8964445979
1.7603-1.81710.254907060731170.2175607632632779X-RAY DIFFRACTION99.9309868875
1.8171-1.8820.259576378541260.203828663122729X-RAY DIFFRACTION99.7902831178
1.882-1.95740.2505708367291550.1911176691522767X-RAY DIFFRACTION99.9316005472
1.9574-2.04640.2438590833261480.168851722582740X-RAY DIFFRACTION99.8271690287
2.0464-2.15420.2113642321451390.1579840048052793X-RAY DIFFRACTION99.9318336742
2.1542-2.28910.2280434228281580.1656074700832731X-RAY DIFFRACTION99.9308197855
2.2891-2.46570.2221380349731680.1655673957552769X-RAY DIFFRACTION99.9659632403
2.4657-2.71350.2256482302221680.167789347552771X-RAY DIFFRACTION100
2.7135-3.10540.2250998733721410.1618651887182812X-RAY DIFFRACTION99.9661475965
3.1054-3.90960.1868311585361350.1376551493022867X-RAY DIFFRACTION100
3.9096-23.7000960.1374010619931500.1388747554232975X-RAY DIFFRACTION99.8721636306

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