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- PDB-7wuw: Crystal structure of AziU3/U2 from Streptomyces sahachiroi -

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Basic information

Entry
Database: PDB / ID: 7wuw
TitleCrystal structure of AziU3/U2 from Streptomyces sahachiroi
Components
  • AziU2
  • AziU3
KeywordsBIOSYNTHETIC PROTEIN / Complex / New Fold / Aziridine synthase / Azinomycin B
Function / homologyButirosin biosynthesis protein H, N-terminal / Butirosin biosynthesis protein H, N-terminal / Azi28 / Azi29
Function and homology information
Biological speciesStreptomyces sahachiroi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsKurosawa, S. / Yoshida, A. / Tomita, T. / Nishiyama, M.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24228001 Japan
Japan Society for the Promotion of Science (JSPS)17H06168 Japan
Japan Science and TechnologyJPMJSP2108 Japan
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Molecular Basis for Enzymatic Aziridine Formation via Sulfate Elimination.
Authors: Kurosawa, S. / Hasebe, F. / Okamura, H. / Yoshida, A. / Matsuda, K. / Sone, Y. / Tomita, T. / Shinada, T. / Takikawa, H. / Kuzuyama, T. / Kosono, S. / Nishiyama, M.
History
DepositionFeb 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2022Group: 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
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AziU2
B: AziU2
C: AziU3
D: AziU3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,9458
Polymers128,6784
Non-polymers2674
Water18,5731031
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11210 Å2
ΔGint-44 kcal/mol
Surface area36370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.851, 132.203, 157.015
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AziU2 / Azi28


Mass: 25401.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sahachiroi (bacteria) / Plasmid: pET Duet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: B4XYC0
#2: Protein AziU3 / Azi29


Mass: 38937.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sahachiroi (bacteria) / Plasmid: pET Duet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: B4XYC1
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1031 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% PEG 3350, 0.2M Magnesium formic acid

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.75→48.711 Å / Num. obs: 115932 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.096 / Net I/σ(I): 14.4
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 5707 / CC1/2: 0.824 / Rrim(I) all: 0.861 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
REFMAC5.8.0258refinement
RefinementMethod to determine structure: SAD / Resolution: 1.75→48.711 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / Cross valid method: FREE R-VALUE / ESU R: 0.107 / ESU R Free: 0.101
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1956 5707 4.927 %
Rwork0.169 110131 -
all0.17 --
obs-115838 99.896 %
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: 19.401 Å2
Baniso -1Baniso -2Baniso -3
1--0.775 Å2-0 Å2-0 Å2
2---1.245 Å20 Å2
3---2.02 Å2
Refinement stepCycle: LAST / Resolution: 1.75→48.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8159 0 16 1032 9207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0138522
X-RAY DIFFRACTIONr_bond_other_d0.0350.0177704
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.63811681
X-RAY DIFFRACTIONr_angle_other_deg2.3211.56817735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52551083
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.15720484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.796151195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9281586
X-RAY DIFFRACTIONr_chiral_restr0.0470.21086
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029828
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021998
X-RAY DIFFRACTIONr_nbd_refined0.1910.21555
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.27035
X-RAY DIFFRACTIONr_nbtor_refined0.1520.23987
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0610.23603
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2829
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1890.221
X-RAY DIFFRACTIONr_nbd_other0.1740.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0820.224
X-RAY DIFFRACTIONr_mcbond_it0.6321.9824260
X-RAY DIFFRACTIONr_mcbond_other0.631.9824259
X-RAY DIFFRACTIONr_mcangle_it1.0752.9685331
X-RAY DIFFRACTIONr_mcangle_other1.0762.9695332
X-RAY DIFFRACTIONr_scbond_it0.8012.074262
X-RAY DIFFRACTIONr_scbond_other0.8012.0714263
X-RAY DIFFRACTIONr_scangle_it1.3173.0756338
X-RAY DIFFRACTIONr_scangle_other1.3173.0766339
X-RAY DIFFRACTIONr_lrange_it3.42724.0729734
X-RAY DIFFRACTIONr_lrange_other3.13623.3119416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.7950.2764310.2398010X-RAY DIFFRACTION99.8935
1.795-1.8450.2344610.2217849X-RAY DIFFRACTION100
1.845-1.8980.2333960.2097640X-RAY DIFFRACTION99.9876
1.898-1.9560.2383660.2017460X-RAY DIFFRACTION100
1.956-2.0210.2123360.1857219X-RAY DIFFRACTION100
2.021-2.0920.2183800.1786938X-RAY DIFFRACTION99.9727
2.092-2.170.2013450.1716749X-RAY DIFFRACTION99.9296
2.17-2.2590.1962970.1616504X-RAY DIFFRACTION99.8825
2.259-2.360.1983040.166259X-RAY DIFFRACTION99.9239
2.36-2.4750.1963280.1615959X-RAY DIFFRACTION99.9841
2.475-2.6080.2173150.1725677X-RAY DIFFRACTION99.9666
2.608-2.7670.2132610.1595402X-RAY DIFFRACTION99.9823
2.767-2.9580.1972510.1685076X-RAY DIFFRACTION100
2.958-3.1940.1812580.1644741X-RAY DIFFRACTION99.8402
3.194-3.4990.1872220.1634375X-RAY DIFFRACTION99.9565
3.499-3.9120.1692300.1543968X-RAY DIFFRACTION99.9286
3.912-4.5170.1441720.143531X-RAY DIFFRACTION99.946
4.517-5.5310.1741670.1513020X-RAY DIFFRACTION100
5.531-7.8170.1831250.1772375X-RAY DIFFRACTION99.8801
7.817-48.7110.2620.1721379X-RAY DIFFRACTION98.2947

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