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- PDB-9j2m: Fe2+/pterin-dependent enzyme,BH4-SnPolE complex -

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Basic information

Entry
Database: PDB / ID: 9j2m
TitleFe2+/pterin-dependent enzyme,BH4-SnPolE complex
ComponentsSnPolE
KeywordsOXIDOREDUCTASE / Fe2+/pterin-dependent
Function / homologyProtein of unknown function DUF6421 / Family of unknown function (DUF6421) / : / 5,6,7,8-TETRAHYDROBIOPTERIN / Uncharacterized protein
Function and homology information
Biological speciesStreptomyces sp. NTH33 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 7, 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

Downloads & links

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Assembly

Deposited unit
A: SnPolE
B: SnPolE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2116
Polymers85,6172
Non-polymers5944
Water9,440524
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-36 kcal/mol
Surface area30480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.674, 91.364, 113.116
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 SnPolE


Mass: 42808.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. NTH33 (bacteria) / Gene: C1I97_07030 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2W2MBS7
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-H4B / 5,6,7,8-TETRAHYDROBIOPTERIN


Mass: 241.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N5O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium bromide 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: Mar 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.65→18.12 Å / Num. obs: 101684 / % possible obs: 97.99 % / Redundancy: 9.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.08302 / Net I/σ(I): 15.08
Reflection shellResolution: 1.65→1.709 Å / Rmerge(I) obs: 0.5266 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 9323 / CC1/2: 0.807

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→18.12 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2236 5010 4.94 %
Rwork0.2042 --
obs0.2052 101446 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→18.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5994 0 36 524 6554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076174
X-RAY DIFFRACTIONf_angle_d0.9228380
X-RAY DIFFRACTIONf_dihedral_angle_d7.623836
X-RAY DIFFRACTIONf_chiral_restr0.054908
X-RAY DIFFRACTIONf_plane_restr0.0111106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.27121300.24362888X-RAY DIFFRACTION88
1.67-1.690.2311310.22623001X-RAY DIFFRACTION91
1.69-1.710.23741540.22153011X-RAY DIFFRACTION94
1.71-1.730.22921630.20253096X-RAY DIFFRACTION95
1.73-1.750.23491480.2123161X-RAY DIFFRACTION98
1.75-1.780.241610.213229X-RAY DIFFRACTION99
1.78-1.80.22951590.20893236X-RAY DIFFRACTION100
1.8-1.830.24261650.20993233X-RAY DIFFRACTION100
1.83-1.860.20321590.21823270X-RAY DIFFRACTION100
1.86-1.890.25041740.24823261X-RAY DIFFRACTION100
1.89-1.920.46651480.47252946X-RAY DIFFRACTION90
1.92-1.960.38951610.30743078X-RAY DIFFRACTION96
1.96-1.990.25251650.21473275X-RAY DIFFRACTION100
1.99-2.030.23111950.19573242X-RAY DIFFRACTION100
2.03-2.080.20351870.18923244X-RAY DIFFRACTION100
2.08-2.130.22811830.19793244X-RAY DIFFRACTION100
2.13-2.180.19121840.20373253X-RAY DIFFRACTION100
2.18-2.240.2831730.23473139X-RAY DIFFRACTION96
2.24-2.30.38561490.34163117X-RAY DIFFRACTION95
2.3-2.380.24141670.2083251X-RAY DIFFRACTION100
2.38-2.460.2121700.20653289X-RAY DIFFRACTION100
2.46-2.560.23021760.20073284X-RAY DIFFRACTION100
2.56-2.680.22381700.20383296X-RAY DIFFRACTION100
2.68-2.820.23761810.20373258X-RAY DIFFRACTION100
2.82-2.990.21311620.20273318X-RAY DIFFRACTION100
2.99-3.220.22171820.19963301X-RAY DIFFRACTION100
3.22-3.550.19041880.1883311X-RAY DIFFRACTION100
3.55-4.050.18491730.16543340X-RAY DIFFRACTION100
4.05-5.090.17811890.13783363X-RAY DIFFRACTION100
5.09-18.120.15291630.16673501X-RAY DIFFRACTION99

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