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- PDB-8r2j: X-ray crystallographic structure of SwaQ2 in complex with NADP+ a... -

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Basic information

Entry
Database: PDB / ID: 8r2j
TitleX-ray crystallographic structure of SwaQ2 in complex with NADP+ and doxorubicin
ComponentsNmrA family transcriptional regulator
KeywordsBIOSYNTHETIC PROTEIN / Polyketide / antibiotic / biosynthesis
Function / homologyDOXORUBICIN / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Function and homology information
Biological speciesStreptomyces swartbergensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSchnell, R. / Schneider, G.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2018-03999 Sweden
CitationJournal: Acs Catalysis / Year: 2024
Title: Mechanism of Two-Component Mono-Oxygenases Involved in Anthracycline 1-Hydroxylation
Authors: Wandi, B.N. / Dinis, P. / Siitonen, V. / Schneider, G. / Schnell, R. / Metsa-Ketele, M.
History
DepositionNov 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NmrA family transcriptional regulator
B: NmrA family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5378
Polymers62,8762
Non-polymers3,6616
Water5,062281
1
A: NmrA family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2694
Polymers31,4381
Non-polymers1,8303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NmrA family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2694
Polymers31,4381
Non-polymers1,8303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.313, 87.313, 174.382
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein NmrA family transcriptional regulator


Mass: 31438.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The N-terminal His6-tag used for purification was removed, the first residue, Ser1, is a remnant of the expression tag.
Source: (gene. exp.) Streptomyces swartbergensis (bacteria) / Gene: CA983_01310 / Plasmid: pBAD
Details (production host): N-terminal His6-tag, removable by TEV protease
Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-DM2 / DOXORUBICIN / ADRIAMYCIN


Mass: 543.519 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H29NO11 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, chemotherapy*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.05 Å3/Da / Density % sol: 59.5 % / Description: needle
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.67 / Details: 0.1 M NaCacodylate pH6.67, 1M Na3-CITRATE

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 19, 2022 / Details: MIRRORS
RadiationMonochromator: 0.976254 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 2.4→29.08 Å / Num. obs: 27570 / % possible obs: 94.2 % / Redundancy: 4.1 % / Biso Wilson estimate: 39.5 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.087 / Net I/σ(I): 6.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.774 / Mean I/σ(I) obs: 2 / Num. unique obs: 2894 / CC1/2: 0.722 / Rpim(I) all: 0.523 / % possible all: 93.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.08 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 14.709 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.333 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20344 1444 5.3 %RANDOM
Rwork0.16127 ---
obs0.16353 26051 93.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.083 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20.4 Å20 Å2
2--0.79 Å2-0 Å2
3----2.58 Å2
Refinement stepCycle: 1 / Resolution: 2.4→29.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4182 0 252 281 4715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134603
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174186
X-RAY DIFFRACTIONr_angle_refined_deg1.8141.6886326
X-RAY DIFFRACTIONr_angle_other_deg1.3821.5899635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8535558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0820.345261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52915664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7521550
X-RAY DIFFRACTIONr_chiral_restr0.0760.2591
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025214
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021022
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_it1.3392.2542206
X-RAY DIFFRACTIONr_mcbond_other1.3382.2532205
X-RAY DIFFRACTIONr_mcangle_it2.3353.3672754
X-RAY DIFFRACTIONr_mcangle_other2.3353.3682755
X-RAY DIFFRACTIONr_scbond_it1.7892.6582397
X-RAY DIFFRACTIONr_scbond_other1.7892.6582398
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0333.9173566
X-RAY DIFFRACTIONr_long_range_B_refined6.34244.37919200
X-RAY DIFFRACTIONr_long_range_B_other6.28744.10818998
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 103 -
Rwork0.239 1920 -
obs--93.44 %
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)
11.37710.3064-0.20721.2248-0.26282.01920.03210.10440.059-0.0887-0.05220.2093-0.1338-0.48760.02010.17960.0709-0.03560.2218-0.03110.0427-24.8863.29-8.846
20.9058-0.06210.01611.47150.17551.9987-0.0158-0.0496-0.13360.1047-0.0196-0.01950.4410.25850.03540.2060.0960.01250.19190.03670.02487.187-23.82-6.774
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 410
2X-RAY DIFFRACTION2B1 - 410

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