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- PDB-9j3g: Fe2+/pterin-dependent, apo SmPolE -

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Basic information

Entry
Database: PDB / ID: 9j3g
TitleFe2+/pterin-dependent, apo SmPolE
ComponentsSmPolE
KeywordsOXIDOREDUCTASE / Fe2+/pterin-dependent
Function / homologyProtein of unknown function DUF6421 / Family of unknown function (DUF6421) / : / Uncharacterized protein
Function and homology information
Biological speciesStreptomyces sp. ms191 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsZhang, Z.Y. / Chen, W.Q. / Wang, B.J. / Qu, Y. / Gong, R. / Liu, J.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32170026 China
National Natural Science Foundation of China (NSFC)31070027 China
National Natural Science Foundation of China (NSFC)32371303 China
CitationJournal: Nat.Chem. / Year: 2025
Title: A two-metalloenzyme cascade constructs the azetidine-containing pharmacophore.
Authors: Gong, R. / Qu, Y. / Liu, J. / Zhang, X. / Zhou, L. / Tian, Z. / Zeng, X. / Jin, B. / Li, Z. / Yu, L. / Chen, R. / Zhou, Y. / Liao, L. / Yang, L. / Song, X. / Cai, Y.S. / Shen, K. / Deng, Z. ...Authors: Gong, R. / Qu, Y. / Liu, J. / Zhang, X. / Zhou, L. / Tian, Z. / Zeng, X. / Jin, B. / Li, Z. / Yu, L. / Chen, R. / Zhou, Y. / Liao, L. / Yang, L. / Song, X. / Cai, Y.S. / Shen, K. / Deng, Z. / Zhang, Z. / Wang, B. / Chen, W.
History
DepositionAug 8, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2025Group: Database references / Category: citation / Item: _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: SmPolE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8532
Polymers44,7971
Non-polymers561
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-11 kcal/mol
Surface area16670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.251, 83.293, 94.189
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SmPolE


Mass: 44796.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. ms191 (bacteria) / Gene: EAO71_13070 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A652L0K3
#2: Chemical ChemComp-FE2 / FE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.45 Å3/Da / Density % sol: 49.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium thiocynate 0.1 M Bio-tris propane (pH 6.5) 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.87→32.48 Å / Num. obs: 35383 / % possible obs: 100 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.038 / Net I/σ(I): 15.2
Reflection shellResolution: 1.87→1.92 Å / Rmerge(I) obs: 0.917 / Num. unique obs: 2571 / Rrim(I) all: 0.994

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→31.2 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 30.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.266 1705 4.83 %
Rwork0.215 --
obs0.2175 35324 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.87→31.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2981 0 1 160 3142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083076
X-RAY DIFFRACTIONf_angle_d1.0884167
X-RAY DIFFRACTIONf_dihedral_angle_d6.249418
X-RAY DIFFRACTIONf_chiral_restr0.056449
X-RAY DIFFRACTIONf_plane_restr0.014553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.930.43871380.39032736X-RAY DIFFRACTION99
1.93-1.990.39611340.35162767X-RAY DIFFRACTION100
1.99-2.060.34591190.30872803X-RAY DIFFRACTION100
2.06-2.140.32661290.27422768X-RAY DIFFRACTION100
2.14-2.240.29231490.24612753X-RAY DIFFRACTION100
2.24-2.360.28451360.23742793X-RAY DIFFRACTION100
2.36-2.50.29761410.23362770X-RAY DIFFRACTION100
2.5-2.70.27091400.23622796X-RAY DIFFRACTION100
2.7-2.970.26561420.23432812X-RAY DIFFRACTION100
2.97-3.40.2941590.22152801X-RAY DIFFRACTION100
3.4-4.280.23521510.172846X-RAY DIFFRACTION100
4.28-31.20.20951670.16512974X-RAY DIFFRACTION100

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