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- PDB-7v2x: The complex structure of soBcmB and its substrate 1 -

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Basic information

Entry
Database: PDB / ID: 7v2x
TitleThe complex structure of soBcmB and its substrate 1
Componentsdioxygenase
KeywordsOXIDOREDUCTASE / dioxygenases / complex / bicyclomycin / side way
Function / homologyChem-7QX / 2-OXOGLUTARIC ACID / :
Function and homology information
Biological speciesStreptomyces ossamyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.0838742992 Å
AuthorsWu, L. / Zhou, J.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The crystal structure of SoBcmB and its side way substrate
Authors: Wu, L. / Zhou, J.H.
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

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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)37,8445
Polymers37,2911
Non-polymers5524
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-23 kcal/mol
Surface area11950 Å2
Unit cell
Length a, b, c (Å)101.097, 101.097, 130.377
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

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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 , 5 types, 101 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-7QX / (3S,6S)-3-[(2S)-butan-2-yl]-6-[(2R)-2-methyl-2,3-bis(oxidanyl)propyl]piperazine-2,5-dion


Mass: 258.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H22N2O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.0, 2 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.08→47.1302 Å / Num. obs: 23036 / % possible obs: 94.9 % / Redundancy: 31.1 % / Biso Wilson estimate: 38.4256802628 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.104 / Net I/σ(I): 26.7
Reflection shellResolution: 2.08→2.14 Å / Rmerge(I) obs: 1.633 / Num. unique obs: 1769 / CC1/2: 0.863

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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
Resolution: 2.0838742992→47.1301780368 Å / SU ML: 0.223371226136 / Cross valid method: FREE R-VALUE / σ(F): 1.33794794639 / Phase error: 23.9224531452
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.22854407007 1138 4.95299442897 %
Rwork0.192322401687 21838 -
obs0.194042906047 22976 95.1820705083 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.8541370872 Å2
Refinement stepCycle: LAST / Resolution: 2.0838742992→47.1301780368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2223 0 36 98 2357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005756897351972314
X-RAY DIFFRACTIONf_angle_d0.8793733198923134
X-RAY DIFFRACTIONf_chiral_restr0.0494521500515329
X-RAY DIFFRACTIONf_plane_restr0.00529660093711418
X-RAY DIFFRACTIONf_dihedral_angle_d17.92177744771342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0839-2.17870.3086760364461420.2554097280022774X-RAY DIFFRACTION99.5561625128
2.1787-2.29360.3175940868311140.2360496748412328X-RAY DIFFRACTION81.9463087248
2.2936-2.43730.2595598699211440.211152583922795X-RAY DIFFRACTION99.9659863946
2.4373-2.62540.2435664225571530.2168711451882812X-RAY DIFFRACTION99.8652745032
2.6254-2.88960.2573338491921490.2072428716512592X-RAY DIFFRACTION91.2450066578
2.8896-3.30770.2464075643931450.1978581782282868X-RAY DIFFRACTION100
3.3077-4.16690.2181544621131210.1734179574382591X-RAY DIFFRACTION88.9471958019
4.1669-47.130.1921354802011700.1776503314333078X-RAY DIFFRACTION99.87699877
Refinement TLS params.Method: refined / Origin x: 38.7756278357 Å / Origin y: 48.414842226 Å / Origin z: 72.8572824569 Å
111213212223313233
T0.251498937978 Å20.0140168037982 Å20.0232819353544 Å2-0.223927670557 Å2-0.0119184480483 Å2--0.248789565158 Å2
L4.12622110741 °2-2.56514276893 °20.829050387398 °2-3.35601362559 °2-0.853161911627 °2--2.93283165692 °2
S0.209711373806 Å °0.226221919328 Å °-0.0145953721405 Å °-0.402413721578 Å °-0.089219444625 Å °0.123689358206 Å °-0.00154513986618 Å °-0.10511370896 Å °-0.115411869253 Å °
Refinement TLS groupSelection details: all

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