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- PDB-7v2t: The complex structure of SoBcmB and its natural precursor 2 -

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Basic information

Entry
Database: PDB / ID: 7v2t
TitleThe complex structure of SoBcmB and its natural precursor 2
Componentsdioxygenase
KeywordsOXIDOREDUCTASE / complex / bicyclomycin / oxa-bridged eight-membered heterocycle
Function / homologyChem-5UQ / 2-OXOGLUTARIC ACID / :
Function and homology information
Biological speciesStreptomyces ossamyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.20005690487 Å
AuthorsZhou, J.H. / Wu, L.
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 9, 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)38,1439
Polymers37,2911
Non-polymers8528
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-26 kcal/mol
Surface area11940 Å2
Unit cell
Length a, b, c (Å)100.990, 100.990, 131.620
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-1303-

CL

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Components

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Protein , 1 types, 1 molecules A

#1: Protein dioxygenase


Mass: 37291.176 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 , 7 types, 131 molecules

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


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: 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
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-tris pH 6.5, 0.1 M sodium chloride, 1.5 M Ammonium sulfate

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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 PILATUS3 6M / Detector: PIXEL / Date: May 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 2.2→47.145 Å / Num. obs: 20611 / % possible obs: 99.2 % / Redundancy: 12.3 % / Biso Wilson estimate: 28.753682348 Å2 / CC1/2: 0.999 / Net I/σ(I): 31.7
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 0.408 / Num. unique obs: 1627 / CC1/2: 0.935

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Processing

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

7v3o


Resolution: 2.20005690487→47.1446401168 Å / SU ML: 0.225805811921 / Cross valid method: FREE R-VALUE / σ(F): 1.34919097758 / Phase error: 20.2225558703
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.200760778626 1018 4.95184356455 %
Rwork0.166632856903 19540 -
obs0.168385849607 20558 99.060376813 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.2684692845 Å2
Refinement stepCycle: LAST / Resolution: 2.20005690487→47.1446401168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2223 0 52 123 2398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00699014757012345
X-RAY DIFFRACTIONf_angle_d1.142881574663176
X-RAY DIFFRACTIONf_chiral_restr0.139188187151335
X-RAY DIFFRACTIONf_plane_restr0.00514804399236422
X-RAY DIFFRACTIONf_dihedral_angle_d19.47114585951365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.3160.2679418142031490.2095459528182565X-RAY DIFFRACTION94.2034015967
2.316-2.46110.2054164957381330.166663185652756X-RAY DIFFRACTION99.3466299862
2.4611-2.65120.2341111107821470.1660702275052759X-RAY DIFFRACTION99.9312242091
2.6512-2.91790.1993679921821310.1534991590722797X-RAY DIFFRACTION100
2.9179-3.340.1852869559131410.158771825522809X-RAY DIFFRACTION100
3.34-4.20770.183321248031460.1471428921252853X-RAY DIFFRACTION99.9666666667
4.2077-47.10.196588939911710.1842893020593001X-RAY DIFFRACTION99.8112020138

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