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- PDB-8gs1: Crystal structure of AziU2-U3 complex from Streptomyces sahachiro... -

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Basic information

Entry
Database: PDB / ID: 8gs1
TitleCrystal structure of AziU2-U3 complex from Streptomyces sahachiroi NRRL2485
Components
  • Azi28
  • Azi29
KeywordsBIOSYNTHETIC PROTEIN / azinomycin B biosynthetic protein
Function / homologyButirosin biosynthesis protein H, N-terminal / Butirosin biosynthesis protein H, N-terminal / FORMIC ACID / LYSINE / Azi28 / Azi29
Function and homology information
Biological speciesStreptomyces sahachiroi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsCheng, Y. / Li, P. / Liu, W. / Fang, P.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21778064 China
National Natural Science Foundation of China (NSFC)21977107 China
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Oxidase Heterotetramer Completes 1-Azabicyclo[3.1.0]hexane Formation with the Association of a Nonribosomal Peptide Synthetase.
Authors: Cheng, Y. / Yi, X. / Zhang, Y. / He, Q. / Chen, D. / Cao, W. / Fang, P. / Liu, W.
History
DepositionSep 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Azi28
B: Azi29
C: Azi28
D: Azi29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,07527
Polymers124,8144
Non-polymers1,26123
Water7,404411
1
A: Azi28
B: Azi29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,92211
Polymers62,4072
Non-polymers5159
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-12 kcal/mol
Surface area22140 Å2
MethodPISA
2
C: Azi28
D: Azi29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,15316
Polymers62,4072
Non-polymers74614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-11 kcal/mol
Surface area22140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)242.930, 242.930, 135.510
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11C-407-

HOH

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Components

#1: Protein Azi28


Mass: 24087.084 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sahachiroi (bacteria) / Gene: azi28 / Production host: Escherichia coli (E. coli) / References: UniProt: B4XYC0
#2: Protein Azi29


Mass: 38319.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sahachiroi (bacteria) / Gene: azi29 / Production host: Escherichia coli (E. coli) / References: UniProt: B4XYC1
#3: Chemical...
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H15N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 4.62 Å3/Da / Density % sol: 73.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: Sodium formate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 122616 / % possible obs: 99.7 % / Redundancy: 19.8 % / Biso Wilson estimate: 50.21 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.309 / Rpim(I) all: 0.07 / Rrim(I) all: 0.317 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.7-2.77192.7138499944780.5020.6352.7871.299.7
12.37-19.92180.0431060058810.010.04449.676.4

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Processing

Software
NameVersionClassification
PHENIX1.13refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→27.26 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0.34 / Phase error: 24.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2185 6332 5.16 %
Rwork0.187 116284 -
obs0.1886 122616 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.09 Å2 / Biso mean: 54.8501 Å2 / Biso min: 34.7 Å2
Refinement stepCycle: final / Resolution: 2.7→27.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8284 0 83 411 8778
Biso mean--74.71 52.5 -
Num. residues----1069
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7-2.80.36776540.31641158812242
2.8-2.910.33226200.29921164612266
2.91-3.040.31256160.2671161212228
3.04-3.20.29146350.24291164412279
3.2-3.40.28156540.22681160512259
3.4-3.660.24016200.19841164212262
3.66-4.030.20056450.16831161712262
4.03-4.610.15526120.13231166012272
4.61-5.80.16575890.141168612275
5.8-27.260.17636870.1611158412271
Refinement TLS params.Method: refined / Origin x: 47.1481 Å / Origin y: 136.3369 Å / Origin z: 85.0191 Å
111213212223313233
T0.3141 Å20.07 Å20.0083 Å2-0.3253 Å20.0559 Å2--0.3793 Å2
L0.4144 °20.0551 °20.1957 °2-0.4803 °20.1328 °2--1.0776 °2
S-0.0359 Å °0.0201 Å °0.0258 Å °0.0707 Å °0.0019 Å °0.0271 Å °-0.0444 Å °0.1222 Å °0.036 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA18 - 219
2X-RAY DIFFRACTION1allA301 - 302
3X-RAY DIFFRACTION1allB8 - 339
4X-RAY DIFFRACTION1allE401
5X-RAY DIFFRACTION1allB501 - 506
6X-RAY DIFFRACTION1allC19 - 217
7X-RAY DIFFRACTION1allC301 - 306
8X-RAY DIFFRACTION1allD6 - 341
9X-RAY DIFFRACTION1allF401
10X-RAY DIFFRACTION1allD501 - 507
11X-RAY DIFFRACTION1allS1 - 426

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