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- PDB-8xhq: The complex structure of SoBcmC and its natural substrate -

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Basic information

Entry
Database: PDB / ID: 8xhq
TitleThe complex structure of SoBcmC and its natural substrate
ComponentsFe/2OG dependent dioxigenase
KeywordsOXIDOREDUCTASE / hydroxylation / selectivity / bicyclomycin
Function / homology: / 2-OXOGLUTARIC ACID / :
Function and homology information
Biological speciesStreptomyces ossamyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.90000655451 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

Downloads & links

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Assembly

Deposited unit
B: Fe/2OG dependent dioxigenase
A: Fe/2OG dependent dioxigenase
C: Fe/2OG dependent dioxigenase
D: Fe/2OG dependent dioxigenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,48317
Polymers138,6714
Non-polymers1,81213
Water10,485582
1
B: Fe/2OG dependent dioxigenase
D: Fe/2OG dependent dioxigenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2599
Polymers69,3352
Non-polymers9247
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Fe/2OG dependent dioxigenase
C: Fe/2OG dependent dioxigenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2248
Polymers69,3352
Non-polymers8896
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.193, 142.985, 85.441
Angle α, β, γ (deg.)90.000, 92.904, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules BACD

#1: Protein
Fe/2OG dependent dioxigenase


Mass: 34667.742 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: WP_055518629 / Source: (gene. exp.) Streptomyces ossamyceticus (bacteria) / Gene: bcmC / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 595 molecules

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


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-A1LVE / (3S,6S)-3-(2-methylpropyl)-6-[(2S)-4-oxidanylbutan-2-yl]piperazine-2,5-dione


Mass: 242.315 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H22N2O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 582 / 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: 2.25 Å3/Da / Density % sol: 45.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium chloride, 0.1 M Na acetate pH 5, 20% PEG 6000

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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 PILATUS3 6M / Detector: PIXEL / Date: Oct 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.9→47.66 Å / Num. obs: 96038 / % possible obs: 99.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 23.2454491916 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.054 / Net I/σ(I): 10.8
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.767 / Num. unique obs: 4680 / CC1/2: 0.82 / Rpim(I) all: 0.324

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Processing

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

8xhp


Resolution: 1.90000655451→44.8711833682 Å / SU ML: 0.23335783086 / Cross valid method: FREE R-VALUE / σ(F): 1.34669267361 / Phase error: 23.8008865688
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.224449785288 4771 4.97062010335 %
Rwork0.197550431069 91213 -
obs0.198905448739 95984 99.7132765427 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.7813053734 Å2
Refinement stepCycle: LAST / Resolution: 1.90000655451→44.8711833682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9014 0 114 582 9710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007302163020369419
X-RAY DIFFRACTIONf_angle_d0.92529497821512810
X-RAY DIFFRACTIONf_chiral_restr0.05372685849381356
X-RAY DIFFRACTIONf_plane_restr0.006794538762291714
X-RAY DIFFRACTIONf_dihedral_angle_d18.33578871445508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.900006555-1.92160.308739569991650.2708525342182968X-RAY DIFFRACTION99.7770700637
1.9216-1.94420.3394426187941560.2735085885433036X-RAY DIFFRACTION99.75
1.9442-1.96790.2939340881391480.2508537214313079X-RAY DIFFRACTION99.7835497835
1.9679-1.99280.2762826610781820.2455099374342990X-RAY DIFFRACTION99.8112020138
1.9928-2.0190.2607094361451720.2301832183723015X-RAY DIFFRACTION99.843358396
2.019-2.04670.2443436041021840.2295548415093048X-RAY DIFFRACTION99.5073891626
2.0467-2.07590.2539591978481470.2127704068733002X-RAY DIFFRACTION99.6203732996
2.0759-2.10690.2618702317791680.218726001813022X-RAY DIFFRACTION99.8747651847
2.1069-2.13990.2564295484181620.2213358746813094X-RAY DIFFRACTION99.9079472231
2.1399-2.17490.2941325542051640.2132015678042979X-RAY DIFFRACTION99.8411689962
2.1749-2.21240.2722770351291840.2157635545243012X-RAY DIFFRACTION99.9374609131
2.2124-2.25270.273345188761290.2145227790153080X-RAY DIFFRACTION99.7823383085
2.2527-2.2960.2348857852471400.2167647843413039X-RAY DIFFRACTION100
2.296-2.34290.2637981761571400.2120319753323087X-RAY DIFFRACTION99.9380613193
2.3429-2.39380.2647033048621480.2121294224553015X-RAY DIFFRACTION99.9052432091
2.3938-2.44950.253396235131810.2173208267263082X-RAY DIFFRACTION99.847001224
2.4495-2.51070.2321481107271570.2132194168773012X-RAY DIFFRACTION99.4976452119
2.5107-2.57860.2324284869941400.2148374840443067X-RAY DIFFRACTION99.9376752883
2.5786-2.65450.2649053578871380.2196415989623049X-RAY DIFFRACTION99.9686323714
2.6545-2.74010.2779774957481400.2180582704063080X-RAY DIFFRACTION99.8759305211
2.7401-2.83810.2883938659681490.2232246085843091X-RAY DIFFRACTION99.907493062
2.8381-2.95170.2534116557561570.2177707373862995X-RAY DIFFRACTION99.746835443
2.9517-3.0860.2295237171161820.2136199701853034X-RAY DIFFRACTION99.4126738794
3.086-3.24860.2219507300451600.2021837985823031X-RAY DIFFRACTION99.2534992224
3.2486-3.45210.2021393780081810.195475020993035X-RAY DIFFRACTION99.6900185989
3.4521-3.71850.1992928433071500.181507260853052X-RAY DIFFRACTION99.7507788162
3.7185-4.09250.1706686882541310.1609536576733088X-RAY DIFFRACTION99.9068901304
4.0925-4.68420.1474835595771270.147642740833065X-RAY DIFFRACTION99.2228784582
4.6842-5.89940.1842025672691950.1618104213043002X-RAY DIFFRACTION98.8864831426
5.8994-44.871180.1728757918121940.1653933524233064X-RAY DIFFRACTION99.2989942091

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