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- PDB-8k5j: The structure of SenA in complex with N,N,N-trimethyl-histidine -

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Basic information

Entry
Database: PDB / ID: 8k5j
TitleThe structure of SenA in complex with N,N,N-trimethyl-histidine
Componentsselenoneine synthase SenA
KeywordsMETAL BINDING PROTEIN / selenoneine synthase / nonheme iron enzyme
Function / homologyN,N,N-trimethyl-histidine / :
Function and homology information
Biological speciesVariovorax paradoxus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsLiu, M. / Yang, Y. / Huang, J.-W. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32101016 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Structural insights into a novel nonheme iron-dependent oxygenase in selenoneine biosynthesis.
Authors: Liu, M. / Yang, Y. / Huang, J.W. / Dai, L. / Zheng, Y. / Cheng, S. / He, H. / Chen, C.C. / Guo, R.T.
History
DepositionJul 21, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: selenoneine synthase SenA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4494
Polymers47,1031
Non-polymers3463
Water11,187621
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-13 kcal/mol
Surface area17320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.986, 96.355, 62.338
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein selenoneine synthase SenA


Mass: 47102.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Variovorax paradoxus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-AVJ / N,N,N-trimethyl-histidine / Hercynine


Mass: 198.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O2 / Feature type: SUBJECT OF INVESTIGATION
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 621 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG 6000, 0.1 M Tris/HCl pH 8.0, 0.2 M ammonium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→22.48 Å / Num. obs: 97669 / % possible obs: 94.7 % / Redundancy: 4.4 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.02 / Rrim(I) all: 0.045 / Χ2: 0.784 / Net I/σ(I): 30.4
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.137 / Mean I/σ(I) obs: 9.1 / Num. unique obs: 8833 / % possible all: 86.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→22.48 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.055 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15499 4915 5 %RANDOM
Rwork0.12238 ---
obs0.12399 92661 94.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.021 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0 Å20 Å2
2--0.26 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.3→22.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3207 0 21 621 3849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0133356
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172983
X-RAY DIFFRACTIONr_angle_refined_deg2.1391.6424589
X-RAY DIFFRACTIONr_angle_other_deg1.621.5716840
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8125407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.27119.124217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97815454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.561543
X-RAY DIFFRACTIONr_chiral_restr0.1360.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.023903
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02867
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0711.5771619
X-RAY DIFFRACTIONr_mcbond_other3.0711.5751618
X-RAY DIFFRACTIONr_mcangle_it3.1062.3652023
X-RAY DIFFRACTIONr_mcangle_other3.1052.3672024
X-RAY DIFFRACTIONr_scbond_it3.9391.9021737
X-RAY DIFFRACTIONr_scbond_other3.9381.9031738
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4932.7322565
X-RAY DIFFRACTIONr_long_range_B_refined4.6419.9964103
X-RAY DIFFRACTIONr_long_range_B_other4.52318.893933
X-RAY DIFFRACTIONr_rigid_bond_restr5.33536338
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.331 Å
RfactorNum. reflection% reflection
Rfree0.19 319 -
Rwork0.15 5927 -
obs--82.51 %

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