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- PDB-9r43: FAD-dependent oxidoreductase McrA -

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Basic information

Entry
Database: PDB / ID: 9r43
TitleFAD-dependent oxidoreductase McrA
ComponentsMitomycin radical oxidase
KeywordsOXIDOREDUCTASE / Flavin / FAD / natural product / oxidase / mitomycin C
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-NH group of donors; With oxygen as acceptor / FAD binding / oxidoreductase activity / response to antibiotic
Similarity search - Function
: / Oxygen oxidoreductase covalent FAD-binding site / Oxygen oxidoreductases covalent FAD-binding site. / Berberine/berberine-like / Berberine and berberine like / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. ...: / Oxygen oxidoreductase covalent FAD-binding site / Oxygen oxidoreductases covalent FAD-binding site. / Berberine/berberine-like / Berberine and berberine like / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Mitomycin radical oxidase
Similarity search - Component
Biological speciesStreptomyces lavendulae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTjallinks, G. / Mattevi, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Cooperation in Science and Technology (COST) actionCOZYME (CA21162)European Union
CitationJournal: Biorxiv / Year: 2025
Title: Characterization of the Mitomycin C Resistance Protein McrA
Authors: Tjallinks, G. / Dunleavy, T. / Jonker, T. / Angeleri, N. / Mattevi, A. / Fraaije, M.
History
DepositionMay 7, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 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: Mitomycin radical oxidase
B: Mitomycin radical oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,03030
Polymers96,8122
Non-polymers4,21828
Water4,378243
1
A: Mitomycin radical oxidase
hetero molecules

A: Mitomycin radical oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,24332
Polymers96,8122
Non-polymers4,43030
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
2
B: Mitomycin radical oxidase
hetero molecules

B: Mitomycin radical oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,81828
Polymers96,8122
Non-polymers4,00626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Unit cell
Length a, b, c (Å)77.872, 80.490, 163.811
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-685-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Mitomycin radical oxidase


Mass: 48406.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lavendulae (bacteria) / Gene: mcrA / Production host: Escherichia coli (E. coli)
References: UniProt: P43485, Oxidoreductases; Acting on the CH-NH group of donors; With oxygen as acceptor

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Non-polymers , 5 types, 271 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.65 Å3/Da / Density % sol: 53.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M calcium acetate, 0.1 M HEPES pH 7.5 and 40% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.1→72.34 Å / Num. obs: 59607 / % possible obs: 98.4 % / Redundancy: 4.9 % / CC1/2: 0.973 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.056 / Rrim(I) all: 0.127 / Χ2: 0.65 / Net I/σ(I): 6.5
Reflection shellResolution: 2.1→2.16 Å / % possible obs: 99.3 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.899 / Num. measured all: 22436 / Num. unique obs: 4643 / CC1/2: 0.673 / Rpim(I) all: 0.432 / Rrim(I) all: 1.002 / Χ2: 0.27 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→72.34 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.333 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24673 2955 5 %RANDOM
Rwork0.20233 ---
obs0.20468 56594 97.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.533 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2---1.13 Å20 Å2
3---1.58 Å2
Refinement stepCycle: 1 / Resolution: 2.1→72.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6643 0 280 243 7166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0127121
X-RAY DIFFRACTIONr_bond_other_d0.0020.0166608
X-RAY DIFFRACTIONr_angle_refined_deg1.831.8279694
X-RAY DIFFRACTIONr_angle_other_deg0.861.73115153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4065880
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.843569
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55310948
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.21056
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028557
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021617
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.3984.4473534
X-RAY DIFFRACTIONr_mcbond_other4.3894.4443530
X-RAY DIFFRACTIONr_mcangle_it5.7737.9824404
X-RAY DIFFRACTIONr_mcangle_other5.7737.9824405
X-RAY DIFFRACTIONr_scbond_it5.5685.0443587
X-RAY DIFFRACTIONr_scbond_other5.5675.0443588
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9738.9885291
X-RAY DIFFRACTIONr_long_range_B_refined9.94551.57894
X-RAY DIFFRACTIONr_long_range_B_other9.94551.547872
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 215 -
Rwork0.302 4189 -
obs--98.99 %

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