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- PDB-9si5: Crystal structure of DoxA in complex with reaction intermediate DHD -

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Basic information

Entry
Database: PDB / ID: 9si5
TitleCrystal structure of DoxA in complex with reaction intermediate DHD
ComponentsCytochrome P-450 monooxygenase DoxA
KeywordsTRANSFERASE / P450 / Oxygenase / reaction intermediate sanpshot / tetracyclin biosynthesis
Function / homology
Function and homology information


13-deoxydaunorubicin hydroxylase / daunorubicin biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / iron ion binding / heme binding / cytoplasm
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
: / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P-450 monooxygenase DoxA
Similarity search - Component
Biological speciesStreptomyces peucetius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsKim, R.Q. / Metsa-Ketela, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Metabolic Engineering of Doxorubicin Biosynthesis: Advancing P450 Catalysis through Redox Partner Optimization and Structural Analysis of DoxA
Authors: Koroleva, A. / Artukka, E. / Yamada, K. / Newmister, S.A. / Sherman, D.H. / Kim, R.Q. / Metsa-Ketela, M.
History
DepositionAug 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 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: Cytochrome P-450 monooxygenase DoxA
D: Cytochrome P-450 monooxygenase DoxA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,6886
Polymers99,3962
Non-polymers2,2924
Water2,450136
1
A: Cytochrome P-450 monooxygenase DoxA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8443
Polymers49,6981
Non-polymers1,1462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Cytochrome P-450 monooxygenase DoxA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8443
Polymers49,6981
Non-polymers1,1462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.873, 108.058, 179.772
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 4 - 422 / Label seq-ID: 39 - 457

Dom-IDAuth asym-IDLabel asym-ID
1AA
2DB

NCS ensembles : (Details: Global NCS restraints between domains: 1 2)
NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.038087, 0.999251, 0.006803), (0.998708, 0.038294, -0.033405), (-0.03364, 0.005522, -0.999419)-52.55289, -0.02665, 46.20292

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Components

#1: Protein Cytochrome P-450 monooxygenase DoxA / 13-deoxycarminomycin C-13 hydroxylase / 13-deoxydaunorubicin C-13 hydroxylase / 13- ...13-deoxycarminomycin C-13 hydroxylase / 13-deoxydaunorubicin C-13 hydroxylase / 13-dihydrocarminomycin C-13 hydroxylase / 13-dihydrodaunorubicin C-13 hydroxylase


Mass: 49698.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces peucetius (bacteria) / Gene: doxA / Production host: Escherichia coli (E. coli)
References: UniProt: Q9ZAU3, 13-deoxydaunorubicin hydroxylase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1JN3 / (7~{S},9~{S})-7-[(2~{R},4~{S},5~{S},6~{S})-4-azanyl-6-methyl-5-oxidanyl-oxan-2-yl]oxy-4-methoxy-6,9,11-tris(oxidanyl)-9-[(1~{R})-1-oxidanylethyl]-8,10-dihydro-7~{H}-tetracene-5,12-dione


Mass: 529.536 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H31NO10 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.49 Å3/Da / Density % sol: 50.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1M MES pH6.0; 0.2M NH4Cl; 20% (w/v) PEG6000

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 18, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.54→89.89 Å / Num. obs: 32896 / % possible obs: 99.4 % / Redundancy: 6.6 % / CC1/2: 0.874 / Rmerge(I) obs: 0.304 / Rpim(I) all: 0.188 / Rrim(I) all: 0.359 / Net I/σ(I): 2.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.8-89.896.30.1118930.670.0720.133
2.54-2.655.32.0938050.4721.452.563

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.105)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→89.89 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.91 / SU B: 46.725 / SU ML: 0.422 / Cross valid method: FREE R-VALUE / ESU R: 0.714 / ESU R Free: 0.336
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.281 1640 5.013 %
Rwork0.2335 31074 -
all0.236 --
obs-32714 98.858 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 69.427 Å2
Baniso -1Baniso -2Baniso -3
1--0.361 Å2-0 Å20 Å2
2--2.496 Å2-0 Å2
3----2.134 Å2
Refinement stepCycle: LAST / Resolution: 2.54→89.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6287 0 162 136 6585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0126631
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166215
X-RAY DIFFRACTIONr_angle_refined_deg2.3311.8549087
X-RAY DIFFRACTIONr_angle_other_deg0.7781.76314249
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3115810
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.3125100
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg2.1154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.73910978
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.6510293
X-RAY DIFFRACTIONr_chiral_restr0.0890.2991
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028178
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021550
X-RAY DIFFRACTIONr_nbd_refined0.2620.21728
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2270.26347
X-RAY DIFFRACTIONr_nbtor_refined0.1990.23257
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0940.23588
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2450.2240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2690.213
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.360.228
X-RAY DIFFRACTIONr_nbd_other0.3170.283
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2690.27
X-RAY DIFFRACTIONr_mcbond_it2.9352.2993252
X-RAY DIFFRACTIONr_mcbond_other2.9352.33252
X-RAY DIFFRACTIONr_mcangle_it4.8824.1144058
X-RAY DIFFRACTIONr_mcangle_other4.8814.1144059
X-RAY DIFFRACTIONr_scbond_it3.1832.5813379
X-RAY DIFFRACTIONr_scbond_other3.1822.5823380
X-RAY DIFFRACTIONr_scangle_it5.2244.6065029
X-RAY DIFFRACTIONr_scangle_other5.2244.6075030
X-RAY DIFFRACTIONr_lrange_it9.10424.6397657
X-RAY DIFFRACTIONr_lrange_other9.08824.197654
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: tight positional; tight thermal / Rms dev Biso : 7.87353 Å2 / Rms dev position: 0.22586 Å / Weight Biso : 0.5 / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2D
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.6060.4041190.4392071X-RAY DIFFRACTION91.0603
2.606-2.6780.4361130.4112217X-RAY DIFFRACTION98.3537
2.678-2.7550.422890.3922197X-RAY DIFFRACTION99.1327
2.755-2.840.3481030.3622105X-RAY DIFFRACTION99.2806
2.84-2.9330.3121180.3161998X-RAY DIFFRACTION99.2961
2.933-3.0360.4131040.2891978X-RAY DIFFRACTION99.0014
3.036-3.150.342960.2761898X-RAY DIFFRACTION99.3523
3.15-3.2790.3341040.2441857X-RAY DIFFRACTION99.4422
3.279-3.4240.359860.2481754X-RAY DIFFRACTION99.675
3.424-3.5910.266890.2291709X-RAY DIFFRACTION99.9444
3.591-3.7850.255990.2281603X-RAY DIFFRACTION99.7655
3.785-4.0140.278810.2131525X-RAY DIFFRACTION99.7515
4.014-4.2910.251670.1911456X-RAY DIFFRACTION99.6728
4.291-4.6340.217830.161368X-RAY DIFFRACTION100
4.634-5.0740.172630.1571232X-RAY DIFFRACTION99.9228
5.074-5.6710.251670.1861146X-RAY DIFFRACTION99.8354
5.671-6.5440.318660.208983X-RAY DIFFRACTION99.8097
6.544-8.0040.224430.172868X-RAY DIFFRACTION99.8904
8.004-11.2750.186370.138688X-RAY DIFFRACTION99.8623
11.275-89.890.246130.301421X-RAY DIFFRACTION99.7701
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9960.3630.48631.24330.78431.7030.0578-0.0487-0.064-0.0071-0.07520.0163-0.0186-0.12770.01730.0026-0.0112-0.00510.61840.03670.4034-7.826532.524813.6667
21.9780.6215-1.22241.5418-0.72083.0551-0.1752-0.223-0.32340.0202-0.0849-0.21660.17020.2770.26010.1224-0.03060.02010.75960.03270.592331.888245.724531.7189
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAp4 - 502
2X-RAY DIFFRACTION2ALLDp3 - 502

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