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- PDB-9j3v: Fe2+/Fe2+ PolF-L-isoleucine complex -

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Basic information

Entry
Database: PDB / ID: 9j3v
TitleFe2+/Fe2+ PolF-L-isoleucine complex
ComponentsPutative molybdopterin oxidoreductase
KeywordsOXIDOREDUCTASE / nonheme diiron enzyme
Function / homologyProtein of unknown function DUF6202 / Family of unknown function (DUF6202) / : / ISOLEUCINE / Putative molybdopterin oxidoreductase
Function and homology information
Biological speciesStreptomyces asoensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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)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 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: Putative molybdopterin oxidoreductase
B: Putative molybdopterin oxidoreductase
C: Putative molybdopterin oxidoreductase
D: Putative molybdopterin oxidoreductase
E: Putative molybdopterin oxidoreductase
F: Putative molybdopterin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,61923
Polymers180,2936
Non-polymers1,32617
Water5,062281
1
A: Putative molybdopterin oxidoreductase
B: Putative molybdopterin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5838
Polymers60,0982
Non-polymers4866
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-75 kcal/mol
Surface area20540 Å2
MethodPISA
2
C: Putative molybdopterin oxidoreductase
D: Putative molybdopterin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5838
Polymers60,0982
Non-polymers4866
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-71 kcal/mol
Surface area20460 Å2
MethodPISA
3
E: Putative molybdopterin oxidoreductase
F: Putative molybdopterin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4527
Polymers60,0982
Non-polymers3555
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-73 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.852, 120.876, 89.221
Angle α, β, γ (deg.)90.00, 91.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative molybdopterin oxidoreductase


Mass: 30048.781 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces asoensis (bacteria) / Gene: polF / Production host: Escherichia coli (E. coli) / References: UniProt: C1IC29
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-ILE / ISOLEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.68 Å3/Da / Density % sol: 54.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium sulfate monohydrate 0.1 M HEPES (pH 7.3) 23% PEG3350

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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: 2.6→24.75 Å / Num. obs: 55934 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.059 / Net I/σ(I): 13.1
Reflection shellResolution: 2.6→2.68 Å / Rmerge(I) obs: 0.932 / Num. unique obs: 4553 / Rpim(I) all: 0.572

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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: 2.6→24.74 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2481 5552 9.93 %
Rwork0.2275 --
obs0.2296 55904 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→24.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11566 0 57 281 11904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611923
X-RAY DIFFRACTIONf_angle_d1.21616284
X-RAY DIFFRACTIONf_dihedral_angle_d10.1911707
X-RAY DIFFRACTIONf_chiral_restr0.0491893
X-RAY DIFFRACTIONf_plane_restr0.0182146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.630.34791770.33461653X-RAY DIFFRACTION100
2.63-2.660.34091610.30941683X-RAY DIFFRACTION100
2.66-2.690.30041700.31391716X-RAY DIFFRACTION100
2.69-2.730.3481740.32991676X-RAY DIFFRACTION100
2.73-2.760.31661850.31111651X-RAY DIFFRACTION100
2.76-2.80.30992060.31721666X-RAY DIFFRACTION100
2.8-2.840.30061900.31491664X-RAY DIFFRACTION100
2.84-2.880.31491960.31591667X-RAY DIFFRACTION100
2.88-2.930.34582030.32671618X-RAY DIFFRACTION100
2.93-2.980.35751840.31221698X-RAY DIFFRACTION100
2.98-3.030.32461830.3091674X-RAY DIFFRACTION100
3.03-3.080.33821620.29261698X-RAY DIFFRACTION100
3.08-3.140.27681740.27821684X-RAY DIFFRACTION100
3.14-3.20.33422110.291651X-RAY DIFFRACTION100
3.21-3.270.29781870.27221670X-RAY DIFFRACTION100
3.27-3.350.29871840.26931662X-RAY DIFFRACTION100
3.35-3.430.29212060.28911691X-RAY DIFFRACTION100
3.43-3.530.30641870.26981639X-RAY DIFFRACTION100
3.53-3.630.29341860.24531671X-RAY DIFFRACTION100
3.63-3.750.23761600.22711718X-RAY DIFFRACTION100
3.75-3.880.26141900.22181688X-RAY DIFFRACTION100
3.88-4.040.23661860.19791666X-RAY DIFFRACTION100
4.04-4.220.2261890.18161670X-RAY DIFFRACTION100
4.22-4.440.19251440.17321730X-RAY DIFFRACTION100
4.44-4.710.23041580.18721712X-RAY DIFFRACTION100
4.72-5.080.19661920.18511695X-RAY DIFFRACTION100
5.08-5.580.26492060.21181667X-RAY DIFFRACTION100
5.58-6.380.21651800.21231704X-RAY DIFFRACTION100
6.38-7.990.17192130.18781669X-RAY DIFFRACTION100
7.99-24.740.15282080.14631701X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 61.1591 Å / Origin y: 44.1766 Å / Origin z: 64.8889 Å
111213212223313233
T0.3486 Å2-0.0084 Å20.0143 Å2-0.3791 Å20.0271 Å2--0.3258 Å2
L0.0914 °20.0504 °20.0745 °2-0.696 °20.2773 °2--0.2352 °2
S0.0229 Å °-0.0053 Å °-0.0082 Å °0.0495 Å °-0.0466 Å °0.0523 Å °0.0645 Å °-0.0485 Å °0 Å °
Refinement TLS groupSelection details: all

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