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- PDB-9s7f: Crystal structure of DoxA in complex with substrate DOD -

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Basic information

Entry
Database: PDB / ID: 9s7f
TitleCrystal structure of DoxA in complex with substrate DOD
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: 1.767 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 4, 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)101,6566
Polymers99,3962
Non-polymers2,2604
Water6,161342
1
A: Cytochrome P-450 monooxygenase DoxA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8283
Polymers49,6981
Non-polymers1,1302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Cytochrome P-450 monooxygenase DoxA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8283
Polymers49,6981
Non-polymers1,1302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.755, 107.708, 184.457
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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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
#3: Chemical ChemComp-A1L3V / (7~{S},9~{S})-7-[(2~{R},4~{S},5~{S},6~{S})-4-azanyl-6-methyl-5-oxidanyl-oxan-2-yl]oxy-9-ethyl-4-methoxy-6,9,11-tris(oxidanyl)-8,10-dihydro-7~{H}-tetracene-5,12-dione


Mass: 513.536 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H31NO9 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1M Citrate pH5.0; 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: 0.873 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.767→74.076 Å / Num. obs: 97832 / % possible obs: 99 % / Redundancy: 4.6 % / CC1/2: 0.986 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.055 / Rrim(I) all: 0.089 / Net I/σ(I): 9.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
9.68-73.9740.0486680.940.0410.06498.5
1.77-1.84.71.12845650.2780.9431.47894.6

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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: 1.767→74.076 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.754 / SU ML: 0.109 / Cross valid method: FREE R-VALUE / ESU R: 0.112 / ESU R Free: 0.108
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2223 4818 4.926 %
Rwork0.1938 92984 -
all0.195 --
obs-97802 98.831 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.48 Å2
Baniso -1Baniso -2Baniso -3
1-2.413 Å20 Å20 Å2
2--1.189 Å2-0 Å2
3----3.601 Å2
Refinement stepCycle: LAST / Resolution: 1.767→74.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6273 0 160 342 6775
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0126613
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166199
X-RAY DIFFRACTIONr_angle_refined_deg2.3251.8569061
X-RAY DIFFRACTIONr_angle_other_deg0.781.76414215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1925808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.4055100
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg2.11454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85710976
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.39310293
X-RAY DIFFRACTIONr_chiral_restr0.1130.2985
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.028162
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021550
X-RAY DIFFRACTIONr_nbd_refined0.2230.21397
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.25616
X-RAY DIFFRACTIONr_nbtor_refined0.1820.23271
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.23424
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2337
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0850.23
X-RAY DIFFRACTIONr_metal_ion_refined0.0760.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2050.216
X-RAY DIFFRACTIONr_nbd_other0.2750.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1720.29
X-RAY DIFFRACTIONr_mcbond_it1.3840.8473244
X-RAY DIFFRACTIONr_mcbond_other1.3840.8473244
X-RAY DIFFRACTIONr_mcangle_it2.1721.5134048
X-RAY DIFFRACTIONr_mcangle_other2.1721.5134049
X-RAY DIFFRACTIONr_scbond_it2.3531.193369
X-RAY DIFFRACTIONr_scbond_other2.3531.1913370
X-RAY DIFFRACTIONr_scangle_it3.5782.0755013
X-RAY DIFFRACTIONr_scangle_other3.5782.0765014
X-RAY DIFFRACTIONr_lrange_it6.59711.26128019
X-RAY DIFFRACTIONr_lrange_other6.58910.92927827
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.767-1.8130.3383120.32566200.32672160.9350.93596.06430.31
1.813-1.8630.3283320.30467100.30570930.940.94999.2810.286
1.863-1.9170.3093490.28164780.28268710.9540.95299.35960.257
1.917-1.9760.2973170.2662950.26266580.9560.95499.30910.236
1.976-2.0410.2673290.24161290.24265070.9580.96999.2470.213
2.041-2.1120.2653150.23959330.24162920.8040.95999.30070.22
2.112-2.1920.2422740.21756850.21860330.9660.97498.77340.195
2.192-2.2810.2292960.19953720.20158360.970.97997.12130.176
2.281-2.3830.2292850.20152140.20256080.9690.97898.05630.183
2.383-2.4990.2312740.19850680.19953560.9630.97999.73860.182
2.499-2.6340.232460.19148620.19351220.9670.9899.72670.178
2.634-2.7930.2252250.19445840.19648280.9740.97999.60650.184
2.793-2.9860.2182580.1943140.19245900.9710.97999.60780.188
2.986-3.2250.2622160.20639960.20942340.9550.97599.48040.21
3.225-3.5320.2222040.18937070.1939350.9660.9899.39010.195
3.532-3.9470.2061720.16833500.16935510.9780.98599.18330.183
3.947-4.5560.1531390.1429770.14131700.9840.98998.29650.163
4.556-5.5750.1651210.14425240.14526930.9870.99198.21760.168
5.575-7.8620.201930.17520050.17621170.9790.98599.10250.198
7.862-74.0760.168610.19211610.19112480.9790.96797.91670.325
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)
11.70770.3007-0.64831.2152-1.09312.77310.0802-0.03940.0272-0.0221-0.1518-0.06150.05970.310.07160.0126-0.0203-0.00650.1981-0.00270.36668.52921.98414.262
21.55340.31460.65131.60450.49972.4502-0.0941-0.1380.07220.0020.04430.1285-0.0102-0.20270.04980.0417-0.0721-0.04810.22630.02220.3902-31.6139.01732.126
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA4 - 422
2X-RAY DIFFRACTION2ALLD3 - 422

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