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- PDB-8hiv: The structure of apo-SoBcmB with Fe(II) and AKG -

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Basic information

Entry
Database: PDB / ID: 8hiv
TitleThe structure of apo-SoBcmB with Fe(II) and AKG
ComponentsFe/2OG dependent dioxygenase
KeywordsOXIDOREDUCTASE / apo-form / bicyclomycin / dioxygenase
Function / homology2-OXOGLUTARIC ACID / :
Function and homology information
Biological speciesStreptomyces ossamyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2000308002 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
DepositionNov 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
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: Fe/2OG dependent dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4933
Polymers37,2911
Non-polymers2022
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-9 kcal/mol
Surface area12320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.677, 101.677, 130.922
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

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Components

#1: Protein Fe/2OG dependent 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 (E. coli)
#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C5H6O5
#3: Chemical ChemComp-FE2 / FE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.63 Å3/Da / Density % sol: 53.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1M Potassium chloride, 0.1M HEPES pH 7, 1M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→44.03 Å / Num. obs: 20954 / % possible obs: 100 % / Redundancy: 12 % / Biso Wilson estimate: 25.061 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.032 / Rrim(I) all: 0.115 / Net I/σ(I): 17.2
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.942 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 1769 / CC1/2: 0.873 / Rpim(I) all: 0.264 / Rrim(I) all: 0.979 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575refinement
xia2data reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2000308002→26.7825539092 Å / SU ML: 0.239438880972 / Cross valid method: FREE R-VALUE / σ(F): 1.33484361805 / Phase error: 21.7743709606
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.221102034271 1108 5.30473500263 %
Rwork0.186932196069 19779 -
obs0.188791274986 20887 99.9664975591 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.0559365877 Å2
Refinement stepCycle: LAST / Resolution: 2.2000308002→26.7825539092 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2135 0 12 105 2252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008526025206322194
X-RAY DIFFRACTIONf_angle_d0.9374610094322967
X-RAY DIFFRACTIONf_chiral_restr0.05497845187312
X-RAY DIFFRACTIONf_plane_restr0.00570997425822396
X-RAY DIFFRACTIONf_dihedral_angle_d9.357825667061280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.200031-2.30010.3123437250991170.250063240272424X-RAY DIFFRACTION99.9606608969
2.3001-2.42130.2675894301921350.2111464798062422X-RAY DIFFRACTION100
2.4213-2.57290.2275243297491560.206432205342398X-RAY DIFFRACTION99.9608610568
2.5729-2.77140.2582993842511420.2114219471472427X-RAY DIFFRACTION99.9610894942
2.7714-3.04990.2592138895751290.2087214077372463X-RAY DIFFRACTION99.9614346317
3.0499-3.49040.2435421535121500.196108753742453X-RAY DIFFRACTION100
3.4904-4.39440.1858511295711370.1609683345182524X-RAY DIFFRACTION100
4.3944-26.78255390.1832723228761420.1646732597532668X-RAY DIFFRACTION99.9288762447

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