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- PDB-7v3n: The complex structure of soBcmB-D307A and its natural precursor 2 -

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Basic information

Entry
Database: PDB / ID: 7v3n
TitleThe complex structure of soBcmB-D307A and its natural precursor 2
Componentsdioxygenase
KeywordsOXIDOREDUCTASE / complex / mutant / bicyclomycin
Function / homologyChem-5UQ / 2-OXOGLUTARIC ACID / :
Function and homology information
Biological speciesStreptomyces ossamyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85001100152 Å
AuthorsWu, L. / Zhou, J.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Catal / Year: 2023
Title: Enzymatic catalysis favours eight-membered over five-membered ring closure in bicyclomycin biosynthesis
Authors: He, J.B. / Wu, L. / Wei, W. / Meng, S. / Liu, Z.T. / Wu, X. / Pan, H.X. / Yang, S. / Liang, Y. / Zhou, J. / Tang, G.L.
History
DepositionAug 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Sep 4, 2024Group: 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.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8165
Polymers37,2471
Non-polymers5684
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-11 kcal/mol
Surface area13720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.460, 114.460, 55.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-1526-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein dioxygenase


Mass: 37247.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces ossamyceticus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 188 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-5UQ / (3S,6S)-3-((R)-2,3-dihydroxy-2-methylpropyl)-6-((S)-4-hydroxybutan-2-yl)piperazine-2,5-dione


Mass: 274.313 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H22N2O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M MES monohydrate pH 6.5, 1.6M Ammonium sulfate, 10% 1.4-dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97913 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97913 Å / Relative weight: 1
ReflectionResolution: 1.85→80.94 Å / Num. obs: 32011 / % possible obs: 99.7 % / Redundancy: 18.8 % / Biso Wilson estimate: 24.8642105118 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.1
Reflection shellResolution: 1.85→1.9 Å / Rmerge(I) obs: 0.561 / Num. unique obs: 2240 / CC1/2: 0.799

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7V3O

7v3o


Resolution: 1.85001100152→80.9354421746 Å / SU ML: 0.135404379973 / Cross valid method: FREE R-VALUE / σ(F): 1.36071500929 / Phase error: 17.458799539
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.193608913227 1662 5.20236641938 %
Rwork0.166155446258 30285 -
obs0.167576180049 31947 99.6009353079 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.7016062295 Å2
Refinement stepCycle: LAST / Resolution: 1.85001100152→80.9354421746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2541 0 37 184 2762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005948672325272665
X-RAY DIFFRACTIONf_angle_d1.15976243483612
X-RAY DIFFRACTIONf_chiral_restr0.138685220209375
X-RAY DIFFRACTIONf_plane_restr0.00502660937682483
X-RAY DIFFRACTIONf_dihedral_angle_d16.94412506651550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.850011002-1.90450.2496171574181260.247647059342395X-RAY DIFFRACTION96.1479786423
1.9045-1.96590.2702382773341450.2040645445052461X-RAY DIFFRACTION99.5416348358
1.9659-2.03620.2082859052631150.1748982878212505X-RAY DIFFRACTION99.8856271445
2.0362-2.11770.18273657411600.1656258936642480X-RAY DIFFRACTION100
2.1177-2.21410.2000022287741260.1577546636382514X-RAY DIFFRACTION100
2.2141-2.33090.195351479071390.1584481060242500X-RAY DIFFRACTION100
2.3309-2.47690.1820812292241230.1613806011952522X-RAY DIFFRACTION100
2.4769-2.66820.2347904170081380.1810437920732528X-RAY DIFFRACTION99.9250374813
2.6682-2.93670.2117171624371430.1743108967922536X-RAY DIFFRACTION100
2.9367-3.36160.2025993497111510.1736049671712540X-RAY DIFFRACTION100
3.3616-4.23530.1674946688241680.1458905358282562X-RAY DIFFRACTION100
4.2353-80.9350.1709573347481280.1597376054162742X-RAY DIFFRACTION99.6527777778

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