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- PDB-7e36: A [6+4]-cycloaddition adduct is the biosynthetic intermediate in ... -

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Basic information

Entry
Database: PDB / ID: 7.0E+36
TitleA [6+4]-cycloaddition adduct is the biosynthetic intermediate in streptoseomycin biosynthesis
Components
  • Alkanesulfonate monooxygenase SsuD/methylene tetrahydromethanopterin reductase-like flavin-dependent oxidoreductase (Luciferase family)
  • FMN-dependent oxidoreductase (Nitrilotriacetate monooxygenase family)
KeywordsOXIDOREDUCTASE / nargenicin / BIOSYNTHETIC PROTEIN / Oxidase
Function / homologyNitrilotriacetate monooxygenase component A/pristinamycin IIA synthase subunit A / : / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / FMN-dependent oxidoreductase (Nitrilotriacetate monooxygenase family) / Alkanesulfonate monooxygenase SsuD/methylene tetrahydromethanopterin reductase-like flavin-dependent oxidoreductase (Luciferase family)
Function and homology information
Biological speciesNocardia tenerifensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, B. / Ge, H.M.
Funding support China, 8items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21572100 China
National Natural Science Foundation of China (NSFC)81522042 China
National Natural Science Foundation of China (NSFC)81773591 China
National Natural Science Foundation of China (NSFC)81421091 China
National Natural Science Foundation of China (NSFC)81500059 China
National Natural Science Foundation of China (NSFC)81673333 China
National Natural Science Foundation of China (NSFC)21672101 China
National Natural Science Foundation of China (NSFC)21661140001 China
CitationJournal: Nat Commun / Year: 2021
Title: A [6+4]-cycloaddition adduct is the biosynthetic intermediate in streptoseomycin biosynthesis.
Authors: Wang, K.B. / Wang, W. / Zhang, B. / Wang, X. / Chen, Y. / Zhu, H.J. / Liang, Y. / Tan, R.X. / Ge, H.M.
History
DepositionFeb 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.2Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alkanesulfonate monooxygenase SsuD/methylene tetrahydromethanopterin reductase-like flavin-dependent oxidoreductase (Luciferase family)
B: FMN-dependent oxidoreductase (Nitrilotriacetate monooxygenase family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,57515
Polymers80,7582
Non-polymers81713
Water8,845491
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-109 kcal/mol
Surface area27710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.280, 104.990, 75.950
Angle α, β, γ (deg.)90.000, 95.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Alkanesulfonate monooxygenase SsuD/methylene tetrahydromethanopterin reductase-like flavin-dependent oxidoreductase (Luciferase family) / NftO2


Mass: 34339.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardia tenerifensis (bacteria) / Strain: NBRC 101015 / Gene: DFR70_1157
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A318JWT9
#2: Protein FMN-dependent oxidoreductase (Nitrilotriacetate monooxygenase family) / NftO1


Mass: 46418.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardia tenerifensis (bacteria) / Strain: NBRC 101015 / Gene: DFR70_1156
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A318JQQ2

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Non-polymers , 6 types, 504 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6 M magnesium sulfate, 0.1 M MES monohydrate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97917 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 2→75.54 Å / Num. obs: 54007 / % possible obs: 99.7 % / Redundancy: 3.3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.063 / Rrim(I) all: 0.119 / Net I/σ(I): 7.3 / Num. measured all: 180663 / Scaling rejects: 305
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
2-2.052.90.5731129739170.6190.3970.71.797.4
8.94-75.5430.03719136330.9960.0240.04414.499.5

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TVL

1tvl


Resolution: 2→51 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2051 1997 3.7 %
Rwork0.1645 51912 -
obs0.166 53909 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.67 Å2 / Biso mean: 33.5148 Å2 / Biso min: 13.03 Å2
Refinement stepCycle: final / Resolution: 2→51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5459 0 39 491 5989
Biso mean--51.24 38.35 -
Num. residues----714
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.25611380.23393598373697
2.05-2.10.24681410.21993663380499
2.1-2.170.28031430.199437193862100
2.17-2.240.24831440.18637273871100
2.24-2.320.22931400.170536543794100
2.32-2.410.22131430.169637083851100
2.41-2.520.21851410.17137143855100
2.52-2.650.22291440.177237153859100
2.65-2.820.23171430.174437373880100
2.82-3.030.19191440.172737203864100
3.03-3.340.2441420.164437123854100
3.34-3.820.19421440.14537273871100
3.82-4.820.1621440.130937403884100
4.82-510.16291460.160937783924100
Refinement TLS params.Method: refined / Origin x: 19.8445 Å / Origin y: 1.5814 Å / Origin z: 12.2308 Å
111213212223313233
T0.1562 Å2-0.0091 Å2-0.0145 Å2-0.1516 Å2-0.0184 Å2--0.1653 Å2
L0.3185 °20.0893 °2-0.2082 °2-0.5043 °2-0.4205 °2--0.8382 °2
S0.0273 Å °-0.0242 Å °0.0374 Å °0.0116 Å °-0.0069 Å °0.0039 Å °-0.0542 Å °0.0215 Å °-0.017 Å °
Refinement TLS groupSelection details: all

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