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- PDB-7wux: Crystal structure of AziU3/U2 complexed with (5S,6S)-O7-sulfo DAD... -

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Basic information

Entry
Database: PDB / ID: 7wux
TitleCrystal structure of AziU3/U2 complexed with (5S,6S)-O7-sulfo DADH from Streptomyces sahachiroi
Components
  • AziU2
  • AziU3
KeywordsBIOSYNTHETIC PROTEIN / ES Complex / New Fold / Aziridine synthase / Azinomycin B
Function / homologyButirosin biosynthesis protein H, N-terminal / Butirosin biosynthesis protein H, N-terminal / Chem-6OI / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / TRIETHYLENE GLYCOL / Azi28 / Azi29
Function and homology information
Biological speciesStreptomyces sahachiroi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 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)129,60811
Polymers128,6784
Non-polymers9307
Water19,3661075
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10940 Å2
ΔGint-31 kcal/mol
Surface area35730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.872, 131.756, 157.702
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 1082 molecules

#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O3
#5: Chemical ChemComp-6OI / (2S,5S,6S)-2,6-bis(azanyl)-5-oxidanyl-7-sulfooxy-heptanoic acid


Mass: 272.276 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16N2O7S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1075 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.22 Å3/Da / Density % sol: 44.47 %
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-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→48.873 Å / Num. obs: 106322 / % possible obs: 99.6 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.032 / Rrim(I) all: 0.06 / Net I/σ(I): 20.4
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.26 / Num. unique obs: 5231 / CC1/2: 0.965 / Rpim(I) all: 0.11 / Rrim(I) all: 0.283

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0267refinement
RefinementMethod to determine structure: SAD / Resolution: 1.8→48.873 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.121 / SU ML: 0.067 / Cross valid method: FREE R-VALUE / ESU R: 0.115 / ESU R Free: 0.108
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1934 5387 5.071 %
Rwork0.1637 100854 -
all0.165 --
obs-106241 99.486 %
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: 18.828 Å2
Baniso -1Baniso -2Baniso -3
1--0.603 Å2-0 Å2-0 Å2
2---0.278 Å20 Å2
3---0.881 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8153 0 58 1075 9286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0138518
X-RAY DIFFRACTIONr_bond_other_d0.0010.0147795
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.6411665
X-RAY DIFFRACTIONr_angle_other_deg1.2141.57117863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56351074
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.13519.896479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.654151182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7851586
X-RAY DIFFRACTIONr_chiral_restr0.050.21090
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029769
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022079
X-RAY DIFFRACTIONr_nbd_refined0.190.21616
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1670.27565
X-RAY DIFFRACTIONr_nbtor_refined0.1550.23977
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.23696
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2890
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0210.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0090.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1530.222
X-RAY DIFFRACTIONr_nbd_other0.1690.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1150.223
X-RAY DIFFRACTIONr_mcbond_it0.6161.9154248
X-RAY DIFFRACTIONr_mcbond_other0.6151.9154247
X-RAY DIFFRACTIONr_mcangle_it1.0262.8675311
X-RAY DIFFRACTIONr_mcangle_other1.0262.8685312
X-RAY DIFFRACTIONr_scbond_it0.7621.9964270
X-RAY DIFFRACTIONr_scbond_other0.7621.9964271
X-RAY DIFFRACTIONr_scangle_it1.2582.9636345
X-RAY DIFFRACTIONr_scangle_other1.2582.9636346
X-RAY DIFFRACTIONr_lrange_it3.31723.3099777
X-RAY DIFFRACTIONr_lrange_other3.31523.2919772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.2253880.1927357X-RAY DIFFRACTION98.9776
1.847-1.8970.2244240.1847142X-RAY DIFFRACTION99.1482
1.897-1.9520.2063560.1787035X-RAY DIFFRACTION99.7975
1.952-2.0120.2313570.1796761X-RAY DIFFRACTION99.3857
2.012-2.0780.213500.1736558X-RAY DIFFRACTION99.3242
2.078-2.1510.1933430.1696374X-RAY DIFFRACTION99.3492
2.151-2.2330.1943180.1666206X-RAY DIFFRACTION99.4361
2.233-2.3240.22960.1555932X-RAY DIFFRACTION99.6321
2.324-2.4270.1773160.1535703X-RAY DIFFRACTION99.4547
2.427-2.5450.2092720.1615496X-RAY DIFFRACTION99.6889
2.545-2.6830.2182820.1645205X-RAY DIFFRACTION99.4923
2.683-2.8460.1932610.1574943X-RAY DIFFRACTION99.6362
2.846-3.0420.192620.1684681X-RAY DIFFRACTION99.7578
3.042-3.2860.2142190.1744340X-RAY DIFFRACTION99.803
3.286-3.5990.1932210.1664014X-RAY DIFFRACTION99.835
3.599-4.0240.1782070.1493627X-RAY DIFFRACTION99.3007
4.024-4.6460.1461750.1383252X-RAY DIFFRACTION99.7381
4.646-5.6890.1661610.1562766X-RAY DIFFRACTION99.9317
5.689-8.040.2051150.1772179X-RAY DIFFRACTION99.3504
8.04-48.8730.183640.181283X-RAY DIFFRACTION98.8261

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