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- PDB-7v3e: The complex structure of soBcmB and its intermediate product 1a -

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Basic information

Entry
Database: PDB / ID: 7v3e
TitleThe complex structure of soBcmB and its intermediate product 1a
Componentsdioxygenase
KeywordsOXIDOREDUCTASE / complex / bicyclomycin / dioxygenase
Function / homologyChem-5WI / 2-OXOGLUTARIC ACID / :
Function and homology information
Biological speciesStreptomyces ossamyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
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
B: dioxygenase
C: dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,37614
Polymers111,8743
Non-polymers1,50211
Water4,342241
1
A: dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7494
Polymers37,2911
Non-polymers4583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8776
Polymers37,2911
Non-polymers5865
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7494
Polymers37,2911
Non-polymers4583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.878, 180.533, 133.298
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-588-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGVALVAL(chain 'A' and (resid 33 through 206 or resid 208 or resid 210 through 312))AA33 - 20633 - 206
12ARGARGARGARG(chain 'A' and (resid 33 through 206 or resid 208 or resid 210 through 312))AA208208
13THRTHRMETMET(chain 'A' and (resid 33 through 206 or resid 208 or resid 210 through 312))AA210 - 312210 - 312
24ARGARGVALVAL(chain 'B' and (resid 33 through 206 or resid 208 or resid 210 through 312))BB33 - 20633 - 206
25ARGARGARGARG(chain 'B' and (resid 33 through 206 or resid 208 or resid 210 through 312))BB208208
26THRTHRMETMET(chain 'B' and (resid 33 through 206 or resid 208 or resid 210 through 312))BB210 - 312210 - 312
37ARGARGVALVAL(chain 'C' and (resid 33 through 206 or resid 208 or resid 210 through 312))CC33 - 20633 - 206
38ARGARGARGARG(chain 'C' and (resid 33 through 206 or resid 208 or resid 210 through 312))CC208208
39THRTHRMETMET(chain 'C' and (resid 33 through 206 or resid 208 or resid 210 through 312))CC210 - 312210 - 312

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein dioxygenase


Mass: 37291.176 Da / Num. of mol.: 3
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, 252 molecules

#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H6O5
#3: Chemical ChemComp-5WI / (3S,6Z)-3-[(2S)-butan-2-yl]-6-[(2R)-2-methyl-2,3-bis(oxidanyl)propylidene]piperazine-2,5-dione


Mass: 256.298 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H20N2O4
#4: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.0M (NH4)2HPO4, 0.1M imidazole pH 8.0, 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97921 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.115→74.74 Å / Num. obs: 67597 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 12.1
Reflection shellResolution: 2.12→2.23 Å / Rmerge(I) obs: 1.157

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Processing

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

7v3o


Resolution: 2.12→17.46 Å / SU ML: 0.259 / Cross valid method: FREE R-VALUE / σ(F): 1.344 / Phase error: 23.872
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.229 3374 5.005 %
Rwork0.217 --
obs0.218 67412 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.43 Å2
Refinement stepCycle: LAST / Resolution: 2.12→17.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6669 0 94 241 7004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046951
X-RAY DIFFRACTIONf_angle_d0.8039417
X-RAY DIFFRACTIONf_dihedral_angle_d17.2834032
X-RAY DIFFRACTIONf_chiral_restr0.05984
X-RAY DIFFRACTIONf_plane_restr0.0041254
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDType
11AX-RAY DIFFRACTIONPOSITIONAL
12BX-RAY DIFFRACTIONPOSITIONAL
13CX-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1151-2.14530.33181620.27262603X-RAY DIFFRACTION100
2.1453-2.17720.28821380.27092658X-RAY DIFFRACTION100
2.1772-2.21120.30021460.25942606X-RAY DIFFRACTION100
2.2112-2.24740.26761680.25342635X-RAY DIFFRACTION100
2.2474-2.2860.26231370.25462640X-RAY DIFFRACTION100
2.286-2.32750.27841370.24842655X-RAY DIFFRACTION100
2.3275-2.37220.26911410.23572635X-RAY DIFFRACTION100
2.3722-2.42050.24921320.23242655X-RAY DIFFRACTION100
2.4205-2.4730.30951310.24532657X-RAY DIFFRACTION100
2.473-2.53030.27651230.23582642X-RAY DIFFRACTION100
2.5303-2.59340.29821370.24732675X-RAY DIFFRACTION100
2.5934-2.66330.29641290.23652677X-RAY DIFFRACTION100
2.6633-2.74140.26811520.22722607X-RAY DIFFRACTION100
2.7414-2.82950.23661570.23332661X-RAY DIFFRACTION100
2.8295-2.93020.26831510.23292661X-RAY DIFFRACTION100
2.9302-3.04690.2331390.23022654X-RAY DIFFRACTION100
3.0469-3.18480.24771410.22512678X-RAY DIFFRACTION100
3.1848-3.35160.24491210.22832698X-RAY DIFFRACTION100
3.3516-3.55990.20411390.20192669X-RAY DIFFRACTION100
3.5599-3.83210.21521460.19842686X-RAY DIFFRACTION100
3.8321-4.21280.1881290.1962697X-RAY DIFFRACTION100
4.2128-4.81120.18241130.18852741X-RAY DIFFRACTION100
4.8112-6.020.19191310.20362758X-RAY DIFFRACTION100
6.02-17.45750.20831740.21442790X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 23.3636 Å / Origin y: 26.8463 Å / Origin z: 190.1889 Å
111213212223313233
T0.245 Å20.0443 Å2-0.0281 Å2-0.2245 Å2-0.0421 Å2--0.2617 Å2
L0.67 °20.2989 °2-0.2346 °2-0.4958 °2-0.1639 °2--0.5969 °2
S0.0006 Å °0.0277 Å °-0.0288 Å °0.1 Å °0.0088 Å °-0.0434 Å °0.0537 Å °0.0856 Å °-0.003 Å °
Refinement TLS groupSelection details: ALL

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