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- PDB-9j27: Fe-SaPolF-L-isoleucine copmplex -

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Basic information

Entry
Database: PDB / ID: 9j27
TitleFe-SaPolF-L-isoleucine copmplex
ComponentsSaPolF
KeywordsOXIDOREDUCTASE / nonheme diiron enzyme
Function / homologyProtein of unknown function DUF6202 / Family of unknown function (DUF6202) / : / ISOLEUCINE / Uncharacterized protein
Function and homology information
Biological speciesStreptomyces armeniacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsZhang, Z.Y. / Chen, W.Q. / Wang, B.J. / Gong, R. / Qu, Y. / Liu, J.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31070027 China
National Natural Science Foundation of China (NSFC)32170026 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 6, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SaPolF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4073
Polymers31,2201
Non-polymers1872
Water82946
1
A: SaPolF
hetero molecules

A: SaPolF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8146
Polymers62,4402
Non-polymers3744
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area3400 Å2
ΔGint-42 kcal/mol
Surface area21090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.168, 90.168, 64.733
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein SaPolF


Mass: 31219.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces armeniacus (bacteria) / Gene: DVA86_03895 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A345XJU6
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-ILE / ISOLEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.44 Å3/Da / Density % sol: 49.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium malonate (pH 7.0) 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 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: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.2→24.14 Å / Num. obs: 15753 / % possible obs: 99.9 % / Redundancy: 19.2 % / CC1/2: 1 / Rpim(I) all: 0.01378 / Rrim(I) all: 0.061 / Net I/σ(I): 25.4
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 1.221 / Num. unique obs: 1530

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→22.54 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2655 798 5.09 %
Rwork0.2173 --
obs0.2197 15669 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→22.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1918 0 10 46 1974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071967
X-RAY DIFFRACTIONf_angle_d0.8662684
X-RAY DIFFRACTIONf_dihedral_angle_d11.438282
X-RAY DIFFRACTIONf_chiral_restr0.048304
X-RAY DIFFRACTIONf_plane_restr0.009355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.340.3671460.32372411X-RAY DIFFRACTION100
2.34-2.520.30951300.25132475X-RAY DIFFRACTION100
2.52-2.770.35341090.28672484X-RAY DIFFRACTION100
2.77-3.170.32991510.25892437X-RAY DIFFRACTION99
3.17-3.990.25991370.22742466X-RAY DIFFRACTION99
3.99-22.540.20391250.1662598X-RAY DIFFRACTION100

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