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- PDB-7v2u: The complex structure of SoBcmB and its product 2f -

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Basic information

Entry
Database: PDB / ID: 7v2u
TitleThe complex structure of SoBcmB and its product 2f
Componentsdioxygenase
KeywordsOXIDOREDUCTASE / complex / bicyclomycin / dioxygenases
Function / homologyChem-8KI / 2-OXOGLUTARIC ACID / :
Function and homology information
Biological speciesStreptomyces ossamyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.00009920726 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 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)38,0017
Polymers37,2911
Non-polymers7106
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-67 kcal/mol
Surface area12140 Å2
Unit cell
Length a, b, c (Å)101.224, 101.224, 131.898
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-1306-

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 , 6 types, 151 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-8KI / (1S,5S,6S)-5-methyl-1-[(1S,2S)-2-methyl-1,2,3-tris(oxidanyl)propyl]-2-oxa-7,9-diazabicyclo[4.2.2]decane-8,10-dione


Mass: 288.297 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H20N2O6 / Feature type: SUBJECT OF INVESTIGATION
#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 52.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES pH 7.0, 1 M Ammonium sulfate, 1 M potassium chloride

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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→19.8814 Å / Num. obs: 27599 / % possible obs: 99.9 % / Redundancy: 37.8 % / Biso Wilson estimate: 28.0304270345 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.124 / Net I/σ(I): 29
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 1.234 / Num. unique obs: 1988 / CC1/2: 0.936

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7V2T

7v2t


Resolution: 2.00009920726→19.8813893511 Å / SU ML: 0.246244257304 / Cross valid method: FREE R-VALUE / σ(F): 1.33426252639 / Phase error: 23.5245866373
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.214943662032 1377 5.0841825432 %
Rwork0.186388746207 25707 -
obs0.187814111561 27084 98.3013937282 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.1766400392 Å2
Refinement stepCycle: LAST / Resolution: 2.00009920726→19.8813893511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2223 0 54 145 2422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006774553354482337
X-RAY DIFFRACTIONf_angle_d0.8750896640143169
X-RAY DIFFRACTIONf_chiral_restr0.0503836215671332
X-RAY DIFFRACTIONf_plane_restr0.00583050390817422
X-RAY DIFFRACTIONf_dihedral_angle_d16.81178159431361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.07150.3173692699341390.2853411557972445X-RAY DIFFRACTION96.2383612663
2.0715-2.15440.3440913829561480.2832313116152445X-RAY DIFFRACTION95.8240946046
2.1544-2.25230.3071900845681390.2379507339212452X-RAY DIFFRACTION96.0697070819
2.2523-2.37080.2774626507321240.229023884642474X-RAY DIFFRACTION95.6553755523
2.3708-2.51910.2251921558671330.1897074423772586X-RAY DIFFRACTION100
2.5191-2.71320.2542261252281170.1901935303612593X-RAY DIFFRACTION99.7056659308
2.7132-2.98540.2281662672141360.173535299232622X-RAY DIFFRACTION100
2.9854-3.41550.184021564831550.1661577671412599X-RAY DIFFRACTION99.9637023593
3.4155-4.2960.167537611571490.1567442020012651X-RAY DIFFRACTION99.4318181818
4.296-19.880.1829411497211370.1759786468282840X-RAY DIFFRACTION99.932863377

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