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- PDB-8xhx: The complex structure of PaBcmG and its natural substrate -

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Basic information

Entry
Database: PDB / ID: 8xhx
TitleThe complex structure of PaBcmG and its natural substrate
ComponentsFe/2OG dependent dioxygenase
KeywordsOXIDOREDUCTASE / C-H activation / Fe/2OG dependent dioxygenase / bicyclomycin
Function / homology: / 2-OXOGLUTARIC ACID / :
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61000421314 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
A: Fe/2OG dependent dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5475
Polymers34,9901
Non-polymers5564
Water6,539363
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)43.835, 77.512, 86.837
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: 34990.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: WP_003100219 / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 367 molecules

#2: 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
#3: Chemical ChemComp-A1LVG / (3~{S},6~{S})-3-(2-methyl-2-oxidanyl-propyl)-6-[(2~{S})-4-oxidanylbutan-2-yl]piperazine-2,5-dione


Mass: 258.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H22N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.11 Å3/Da / Density % sol: 41.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.5, 1.6 M magnesium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.61→19.57 Å / Num. obs: 39138 / % possible obs: 99.9 % / Redundancy: 12.9 % / Biso Wilson estimate: 19.3622529342 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.026 / Net I/σ(I): 20.3
Reflection shellResolution: 1.61→1.64 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.634 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1924 / CC1/2: 0.629 / Rpim(I) all: 0.643 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSVersion February 5, 2021data reduction
XDSVersion February 5, 2021data scaling
PHASER1.11.1_2575phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8XHT

8xht


Resolution: 1.61000421314→19.5659262452 Å / SU ML: 0.172869259993 / Cross valid method: FREE R-VALUE / σ(F): 1.33785529798 / Phase error: 17.3892378453
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.181029595686 1910 4.88766057628 %
Rwork0.155465620996 37168 -
obs0.156701050716 39078 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.6605273938 Å2
Refinement stepCycle: LAST / Resolution: 1.61000421314→19.5659262452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 34 363 2768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005822429579182492
X-RAY DIFFRACTIONf_angle_d0.8986686641273386
X-RAY DIFFRACTIONf_chiral_restr0.0554829203603351
X-RAY DIFFRACTIONf_plane_restr0.00544959680325451
X-RAY DIFFRACTIONf_dihedral_angle_d16.92362163971448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.610004213141-1.65020.3055594872921470.269559648552610X-RAY DIFFRACTION100
1.6502-1.69480.2722505440861340.2188053401592619X-RAY DIFFRACTION100
1.6948-1.74470.2658673461541430.200528583282600X-RAY DIFFRACTION100
1.7447-1.8010.2388489170411400.1934958142742614X-RAY DIFFRACTION100
1.801-1.86530.1984693986011420.1655576882352606X-RAY DIFFRACTION100
1.8653-1.93990.196509065581310.1488176748392640X-RAY DIFFRACTION100
1.9399-2.02810.2094038862571260.1445962612672622X-RAY DIFFRACTION100
2.0281-2.13490.1735538710531320.1498515767272636X-RAY DIFFRACTION100
2.1349-2.26850.1683838235781150.1498531621532675X-RAY DIFFRACTION100
2.2685-2.44330.1702549682551530.1484609107792645X-RAY DIFFRACTION100
2.4433-2.68860.1656957697241330.1527310784292662X-RAY DIFFRACTION100
2.6886-3.07640.1865912788741490.1587448247342663X-RAY DIFFRACTION100
3.0764-3.8710.153071064211330.1414396876792729X-RAY DIFFRACTION100
3.871-19.56590.1614620823531320.1485953440352847X-RAY DIFFRACTION100

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