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- PDB-9j28: Fe2+-SzPolF-2 complex -

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Basic information

Entry
Database: PDB / ID: 9j28
TitleFe2+-SzPolF-2 complex
ComponentsSzPolF
KeywordsOXIDOREDUCTASE / nonheme diiron enzyme
Function / homologyProtein of unknown function DUF6202 / Family of unknown function (DUF6202) / : / : / Uncharacterized protein
Function and homology information
Biological speciesStreptomyces sp. Z26 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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)31070027 China
National Natural Science Foundation of China (NSFC)31070026 China
National Natural Science Foundation of China (NSFC)32170026 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 6, 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

Downloads & links

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Assembly

Deposited unit
A: SzPolF
B: SzPolF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8006
Polymers62,4302
Non-polymers3704
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-44 kcal/mol
Surface area20460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.507, 122.295, 136.190
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 SzPolF


Mass: 31214.986 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. Z26 (bacteria) / Gene: D7M15_25730 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A498DZ08
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-A1EAJ / (~{Z},2~{S})-2-azanyl-3-methyl-pent-3-enoic acid


Mass: 129.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.57 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M calcium acetate hydrate (pH 7.5) 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.2→24.97 Å / Num. obs: 33702 / % possible obs: 99.9 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 13.4
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 1.035 / Num. unique obs: 2915

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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: 2.2→24.97 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2612 1636 4.96 %
Rwork0.217 --
obs0.2192 32975 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→24.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3972 0 20 92 4084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084077
X-RAY DIFFRACTIONf_angle_d0.9335542
X-RAY DIFFRACTIONf_dihedral_angle_d5.46570
X-RAY DIFFRACTIONf_chiral_restr0.047613
X-RAY DIFFRACTIONf_plane_restr0.009735
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.61331180.58742123X-RAY DIFFRACTION80
2.26-2.340.34541340.31632505X-RAY DIFFRACTION97
2.34-2.420.26941240.23892650X-RAY DIFFRACTION100
2.42-2.520.28931300.22132610X-RAY DIFFRACTION100
2.52-2.630.26811180.22612650X-RAY DIFFRACTION100
2.63-2.770.2721440.22512646X-RAY DIFFRACTION100
2.77-2.940.27031580.23912611X-RAY DIFFRACTION100
2.94-3.170.31921560.23872633X-RAY DIFFRACTION100
3.17-3.490.24851340.23042683X-RAY DIFFRACTION100
3.49-3.990.25191490.19252628X-RAY DIFFRACTION99
3.99-5.020.21121220.16552739X-RAY DIFFRACTION100
5.03-24.970.19841490.1792861X-RAY DIFFRACTION100

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