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- PDB-8xht: The apo structure of PaBcmG -

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Basic information

Entry
Database: PDB / ID: 8xht
TitleThe apo structure of PaBcmG
ComponentsFe/2OG dependent dioxygenase
KeywordsOXIDOREDUCTASE / bicyclomycin / C-H activation / Fe/2OG dependent dioxygenase
Function / homology2-OXOGLUTARIC ACID / : / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81953635204 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
B: Fe/2OG dependent dioxygenase
C: Fe/2OG dependent dioxygenase
D: Fe/2OG dependent dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,04715
Polymers139,9614
Non-polymers1,08611
Water17,312961
1
A: Fe/2OG dependent dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2984
Polymers34,9901
Non-polymers3083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fe/2OG dependent dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1523
Polymers34,9901
Non-polymers1622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fe/2OG dependent dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2984
Polymers34,9901
Non-polymers3083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Fe/2OG dependent dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2984
Polymers34,9901
Non-polymers3083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.331, 103.396, 91.072
Angle α, β, γ (deg.)90.000, 89.971, 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

#1: Protein
Fe/2OG dependent dioxygenase


Mass: 34990.238 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: WP_070141843 / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: bcmG / Production host: Escherichia coli B (bacteria)
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 961 / 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: 2.43 Å3/Da / Density % sol: 49.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 4000, 20% v/v glycerol 0.03 M of each NPS (0.3 M sodium nitrate, 0.3 M disodium hydrogen phosphate, 0.3 M ammonium sulfate), 0.1 M MES/imidazole pH 6.5

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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: Jun 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.8195→50 Å / Num. obs: 118876 / % possible obs: 99.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 18.4363046999 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.047 / Net I/σ(I): 14.4
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 3 / Num. unique obs: 5553 / CC1/2: 0.94 / Rpim(I) all: 0.205 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-3000data reduction
HKL-3000data scaling
PHASER1.11.1_2575phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7V3O

7v3o


Resolution: 1.81953635204→42.0593133897 Å / SU ML: 0.204061884415 / Cross valid method: FREE R-VALUE / σ(F): 1.37824549205 / Phase error: 27.7718905222
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.235620845652 5133 4.98925943566 %
Rwork0.199229889596 97748 -
obs0.201063549681 102881 85.7634691853 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.7693974338 Å2
Refinement stepCycle: LAST / Resolution: 1.81953635204→42.0593133897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9210 0 62 961 10233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006436393674029595
X-RAY DIFFRACTIONf_angle_d0.88911527066113017
X-RAY DIFFRACTIONf_chiral_restr0.05064890012671357
X-RAY DIFFRACTIONf_plane_restr0.005225095497931736
X-RAY DIFFRACTIONf_dihedral_angle_d17.20958645895626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81954-1.84020.281919608951080.2590188319822113X-RAY DIFFRACTION56.1141990904
1.8402-1.86190.291554513649700.2473432786262265X-RAY DIFFRACTION57.9260729348
1.8619-1.88460.301570688061010.2500316562852301X-RAY DIFFRACTION60.2609131962
1.8846-1.90840.29775585261380.232771382842304X-RAY DIFFRACTION61.61998486
1.9084-1.93350.2964472199781240.2303596191372416X-RAY DIFFRACTION64.1738251642
1.9335-1.960.2847619075851500.2237567798632505X-RAY DIFFRACTION66.3418290855
1.96-1.9880.2292335669221330.2199610349292585X-RAY DIFFRACTION68.6363636364
1.988-2.01770.2880340245711520.2226379135982686X-RAY DIFFRACTION70.4043661622
2.0177-2.04920.288067618461440.2242662494592784X-RAY DIFFRACTION73.604826546
2.0492-2.08280.2650891082081260.2224162251792883X-RAY DIFFRACTION76.1194029851
2.0828-2.11870.2736659868821440.2148275686133055X-RAY DIFFRACTION79.4387881798
2.1187-2.15730.2665960792011700.2119906331233095X-RAY DIFFRACTION82.8049708344
2.1573-2.19870.2297577601151730.2188798058073277X-RAY DIFFRACTION85.4806739346
2.1987-2.24360.2306209494792000.2198881185863322X-RAY DIFFRACTION89.006823351
2.2436-2.29240.2798063875521960.211208212413497X-RAY DIFFRACTION92.5563909774
2.2924-2.34570.2446255352412000.2116343332493592X-RAY DIFFRACTION95.061418902
2.3457-2.40440.2592968877181770.2129959899563724X-RAY DIFFRACTION97.8429897166
2.4044-2.46940.2370573812392270.2018159798013763X-RAY DIFFRACTION98.9337961815
2.4694-2.5420.265861718652070.2061100192983727X-RAY DIFFRACTION99.5193523906
2.542-2.62410.2682807727711780.1983713385373805X-RAY DIFFRACTION99.749561733
2.6241-2.71790.2264744934641760.2062302267323817X-RAY DIFFRACTION99.7751124438
2.7179-2.82670.2630151882792020.2158956863053791X-RAY DIFFRACTION99.8499624906
2.8267-2.95530.2532221179722090.2129976218293802X-RAY DIFFRACTION99.8506348021
2.9553-3.1110.2356086997931970.2077348807163792X-RAY DIFFRACTION99.6751624188
3.111-3.30590.2284430546952170.1970457806413783X-RAY DIFFRACTION99.850224663
3.3059-3.5610.2348442438812110.1961440690533783X-RAY DIFFRACTION99.80009995
3.561-3.91910.2154203411162270.173377408473770X-RAY DIFFRACTION99.6758104738
3.9191-4.48570.1745284124561640.164936509023870X-RAY DIFFRACTION99.6295381576
4.4857-5.64930.1689131156381900.1648831768413803X-RAY DIFFRACTION99.2789656887
5.6493-42.05930.2319757943672220.1888246671433838X-RAY DIFFRACTION98.6634264885

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