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- PDB-9kdp: Crystal structure of monooxygenase PenE -

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Basic information

Entry
Database: PDB / ID: 9kdp
TitleCrystal structure of monooxygenase PenE
ComponentsAnthrone monooxygenase
KeywordsOXIDOREDUCTASE / Monooxygenase
Function / homologyABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Dimeric alpha-beta barrel / monooxygenase activity / Anthrone monooxygenase
Function and homology information
Biological speciesSaccharothrix espanaensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.592 Å
AuthorsChi, C.B. / Ma, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22307040 China
CitationJournal: Acs Chem.Biol. / Year: 2025
Title: Functional Conservation and Divergence of AlpJ-Family Oxygenases Catalyzing C-C Bond Cleavage in Atypical Angucycline Biosynthesis.
Authors: Shen, S. / Chi, C. / Fan, K. / Zhang, Q. / Xu, Y. / Gao, J. / Hu, H. / Wang, L. / Yang, D. / Ma, M. / Pan, G.
History
DepositionNov 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anthrone monooxygenase
B: Anthrone monooxygenase
C: Anthrone monooxygenase
D: Anthrone monooxygenase


Theoretical massNumber of molelcules
Total (without water)110,6924
Polymers110,6924
Non-polymers00
Water2,864159
1
A: Anthrone monooxygenase


Theoretical massNumber of molelcules
Total (without water)27,6731
Polymers27,6731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Anthrone monooxygenase


Theoretical massNumber of molelcules
Total (without water)27,6731
Polymers27,6731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Anthrone monooxygenase


Theoretical massNumber of molelcules
Total (without water)27,6731
Polymers27,6731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Anthrone monooxygenase


Theoretical massNumber of molelcules
Total (without water)27,6731
Polymers27,6731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.377, 93.757, 172.229
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Anthrone monooxygenase


Mass: 27673.016 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The missing amino acids of chain are missing due to the electron cloud.
Source: (gene. exp.) Saccharothrix espanaensis (bacteria) / Gene: BN6_54770 / Production host: Escherichia coli (E. coli) / References: UniProt: K0K352
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 289.15 K / Method: liquid diffusion
Details: 20% w/v PEG 3350, 2% v/v TacsimateTM pH 5.0, 0.1 M sodium citrate tribasic dihydrate pH 5.6

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Data collection

DiffractionMean temperature: 173.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.59→29.38 Å / Num. obs: 35959 / % possible obs: 99.42 % / Redundancy: 13 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 13
Reflection shellResolution: 2.59→2.69 Å / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 2.75 / Num. unique obs: 3392

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F9P

5f9p


Resolution: 2.592→29.38 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 29.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2821 1958 5.58 %RANDOM
Rwork0.2052 ---
obs0.2094 35097 97.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.592→29.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7303 0 0 159 7462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087463
X-RAY DIFFRACTIONf_angle_d0.9610144
X-RAY DIFFRACTIONf_dihedral_angle_d5.044444
X-RAY DIFFRACTIONf_chiral_restr0.0541134
X-RAY DIFFRACTIONf_plane_restr0.0051321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5922-2.6570.40281240.25092016X-RAY DIFFRACTION84
2.657-2.72880.36561290.24162204X-RAY DIFFRACTION92
2.7288-2.80910.38631340.23232267X-RAY DIFFRACTION95
2.8091-2.89960.31221360.23142305X-RAY DIFFRACTION96
2.8996-3.00320.34321420.23252359X-RAY DIFFRACTION98
3.0032-3.12330.33541380.23772353X-RAY DIFFRACTION98
3.1233-3.26530.2721390.22112402X-RAY DIFFRACTION99
3.2653-3.43720.32631410.21282404X-RAY DIFFRACTION100
3.4372-3.65220.28171430.20962428X-RAY DIFFRACTION100
3.6522-3.93350.26081440.19452437X-RAY DIFFRACTION100
3.9335-4.32830.2571440.18692444X-RAY DIFFRACTION100
4.3283-4.9520.22651460.16312456X-RAY DIFFRACTION100
4.952-6.22920.26281470.20262490X-RAY DIFFRACTION100
6.2292-29.380.24321510.19722574X-RAY DIFFRACTION99

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