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- PDB-7v3o: The structure of Se-SoBcmB with Fe(II)and AKG -

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Basic information

Entry
Database: PDB / ID: 7v3o
TitleThe structure of Se-SoBcmB with Fe(II)and AKG
ComponentsFe/2OG dependent dioxygenase
KeywordsOXIDOREDUCTASE / bicyclomycin / dioxygenase
Function / homology2-OXOGLUTARIC ACID / :
Function and homology information
Biological speciesStreptomyces ossamyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.83004663987 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 1.1Sep 4, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fe/2OG dependent dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7525
Polymers37,4791
Non-polymers2734
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint-14 kcal/mol
Surface area13010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.620, 101.620, 130.570
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-401-

CL

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Components

#1: Protein Fe/2OG dependent dioxygenase


Mass: 37478.750 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)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES pH 7.0, 1M Ammonium sulfate, 1M potassium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.83→44.003 Å / Num. obs: 35775 / % possible obs: 100 % / Redundancy: 35.9 % / Biso Wilson estimate: 35.2437288375 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.066 / Net I/σ(I): 35.6
Reflection shellResolution: 1.83→1.87 Å / Rmerge(I) obs: 1.296 / Num. unique obs: 2162 / CC1/2: 0.804

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD
Starting model: SAD model

Resolution: 1.83004663987→44.0027507663 Å / SU ML: 0.200468763221 / Cross valid method: FREE R-VALUE / σ(F): 1.34746986285 / Phase error: 24.3093980388
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.227084732589 1869 5.23426779063 %
Rwork0.199602671627 33838 -
obs0.201000478528 35707 99.9748012095 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.7304912817 Å2
Refinement stepCycle: LAST / Resolution: 1.83004663987→44.0027507663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2202 0 13 149 2364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008939013667052269
X-RAY DIFFRACTIONf_angle_d0.9770697297213071
X-RAY DIFFRACTIONf_chiral_restr0.0609008605021322
X-RAY DIFFRACTIONf_plane_restr0.00621785611664412
X-RAY DIFFRACTIONf_dihedral_angle_d7.923706751821833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83005-1.87950.3025169552791250.2794926269842575X-RAY DIFFRACTION100
1.8795-1.93480.3032924367761520.2605912693762521X-RAY DIFFRACTION99.9626028422
1.9348-1.99730.3095287687961380.2483759132812566X-RAY DIFFRACTION100
1.9973-2.06870.2787950843751660.2406660686652536X-RAY DIFFRACTION100
2.0687-2.15150.2507473035631370.2421971692852560X-RAY DIFFRACTION99.9629355078
2.1515-2.24940.2816725716451360.230302789762576X-RAY DIFFRACTION100
2.2494-2.3680.2719115738641430.2267112456532575X-RAY DIFFRACTION100
2.368-2.51630.2274898476341530.22592574772568X-RAY DIFFRACTION99.9632623071
2.5163-2.71060.2685913059261290.2284365232682607X-RAY DIFFRACTION100
2.7106-2.98330.2594798603771580.2151487036052601X-RAY DIFFRACTION100
2.9833-3.41490.2044621775771360.2033989340912640X-RAY DIFFRACTION100
3.4149-4.30180.185551084821480.1692113827962666X-RAY DIFFRACTION100
4.3018-440.2052615123121480.171284231592847X-RAY DIFFRACTION99.8333333333

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