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- PDB-7v36: The complex structure of soBcmB and its intermediate product 2a -

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Basic information

Entry
Database: PDB / ID: 7v36
TitleThe complex structure of soBcmB and its intermediate product 2a
Componentsdioxygenase
KeywordsOXIDOREDUCTASE / complex / bicyclomycin / dioxygenase
Function / homologyChem-5P0 / 2-OXOGLUTARIC ACID / :
Function and homology information
Biological speciesStreptomyces ossamyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96009167444 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)38,1139
Polymers37,2911
Non-polymers8218
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-12 kcal/mol
Surface area11910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.905, 100.905, 132.771
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-407-

CL

21A-684-

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, 208 molecules

#2: Chemical ChemComp-5P0 / (3Z,6S)-3-[(2R)-2-methyl-2,3-bis(oxidanyl)propylidene]-6-[(2S)-4-oxidanylbutan-2-yl]piperazine-2,5-dione


Mass: 272.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H20N2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.62 Å3/Da / Density % sol: 52.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris-HCl pH 8.0, 1.5M Ammonium sulfate

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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: Nov 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.96→43.69315 Å / Num. obs: 28436 / % possible obs: 97.8 % / Redundancy: 7.2 % / Biso Wilson estimate: 28.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.103 / Net I/σ(I): 13.9
Reflection shellResolution: 1.96→2.01 Å / Rmerge(I) obs: 1.09 / Num. unique obs: 1990 / CC1/2: 0.719

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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: 1.96009167444→43.6931466844 Å / SU ML: 0.229390896462 / Cross valid method: FREE R-VALUE / σ(F): 1.33647452375 / Phase error: 21.5502153748
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.206003819897 1370 4.82258518727 %
Rwork0.178744101094 27038 -
obs0.180069405563 28408 96.9821111566 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.8761620735 Å2
Refinement stepCycle: LAST / Resolution: 1.96009167444→43.6931466844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2223 0 56 201 2480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006698601354162347
X-RAY DIFFRACTIONf_angle_d0.8785693622723179
X-RAY DIFFRACTIONf_chiral_restr0.050775136928330
X-RAY DIFFRACTIONf_plane_restr0.00528098391986423
X-RAY DIFFRACTIONf_dihedral_angle_d17.90934875291370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9601-2.03010.3342377860311400.279034696532687X-RAY DIFFRACTION98.570432357
2.0301-2.11140.3054909414011340.2671521349582682X-RAY DIFFRACTION98.2554082345
2.1114-2.20750.2604240021791330.2256020365922682X-RAY DIFFRACTION98.3234369542
2.2075-2.32390.3024640826311280.2374475480332667X-RAY DIFFRACTION96.9812630118
2.3239-2.46950.2203290625741420.1887050883462691X-RAY DIFFRACTION97.8245856354
2.4695-2.66010.2219030244851380.1877092225822692X-RAY DIFFRACTION97.6198689203
2.6601-2.92780.2133694007691460.1714637329842684X-RAY DIFFRACTION97.1173644475
2.9278-3.35130.1883769352641320.1594223373952704X-RAY DIFFRACTION96.4297857871
3.3513-4.22170.1743517319271340.144013406042722X-RAY DIFFRACTION95.6463496316
4.2217-43.6930.156025087641430.1605690150452827X-RAY DIFFRACTION93.5433070866

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