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- PDB-7v34: The complex structure of soBcmB and its product 1d -

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Basic information

Entry
Database: PDB / ID: 7v34
TitleThe complex structure of soBcmB and its product 1d
Componentsdioxygenase
KeywordsOXIDOREDUCTASE / complex / oxa-bridged / bicyclomycin / dioxygenase
Function / homologyChem-5NF / 2-OXOGLUTARIC ACID / :
Function and homology information
Biological speciesStreptomyces ossamyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.00016906068 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)37,9287
Polymers37,2911
Non-polymers6376
Water2,846158
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 area12180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.990, 100.990, 131.387
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-647-

HOH

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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 , 6 types, 164 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-5NF / (3S,4S,5S,8S)-8-[(2S)-butan-2-yl]-3-methyl-3,4-bis(oxidanyl)-1-oxa-7,10-diazaspiro[4.5]decane-6,9-dione


Mass: 272.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H20N2O5 / 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.59 Å3/Da / Density % sol: 52.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris pH 8.0, 1.6M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.03315 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03315 Å / Relative weight: 1
ReflectionResolution: 2→47.134 Å / Num. obs: 27428 / % possible obs: 100 % / Redundancy: 26.8 % / Biso Wilson estimate: 28.4297360814 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.124 / Net I/σ(I): 23.3
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 1.022 / Num. unique obs: 1987 / CC1/2: 0.93

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Processing

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

7v3o


Resolution: 2.00016906068→47.1339078039 Å / SU ML: 0.178461340796 / Cross valid method: FREE R-VALUE / σ(F): 1.34621570011 / Phase error: 19.4958476727
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.210143680906 1335 4.87635606531 %
Rwork0.173919730504 26042 -
obs0.175625226054 27377 99.9926951313 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.1718323103 Å2
Refinement stepCycle: LAST / Resolution: 2.00016906068→47.1339078039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 40 158 2436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007449390222242344
X-RAY DIFFRACTIONf_angle_d0.8772540448773178
X-RAY DIFFRACTIONf_chiral_restr0.0529428375738332
X-RAY DIFFRACTIONf_plane_restr0.0053615669163424
X-RAY DIFFRACTIONf_dihedral_angle_d18.46625008441366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0002-2.07170.2602219882771260.2099921892682564X-RAY DIFFRACTION100
2.0717-2.15460.2485929043811420.1982051877132542X-RAY DIFFRACTION100
2.1546-2.25270.2194498371221320.1876318935032535X-RAY DIFFRACTION99.9625187406
2.2527-2.37140.2122854373221280.1803386852252560X-RAY DIFFRACTION100
2.3714-2.520.2262689367131340.1844182683582569X-RAY DIFFRACTION99.9630177515
2.52-2.71450.2375277773211500.1837838825522556X-RAY DIFFRACTION100
2.7145-2.98770.2302242277931280.1810578094782593X-RAY DIFFRACTION100
2.9877-3.41990.1576773000891220.1750701707812632X-RAY DIFFRACTION100
3.4199-4.30820.2274630477331380.1499934847062651X-RAY DIFFRACTION100
4.3082-47.130.1821556823511350.1708409674182840X-RAY DIFFRACTION100

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