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- PDB-9s5v: diFe-Sulerythin_E53D:E126D reduced -

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Basic information

Entry
Database: PDB / ID: 9s5v
TitlediFe-Sulerythin_E53D:E126D reduced
ComponentsdiFe-Sulerythin_E53D:E126D reduced
KeywordsOXIDOREDUCTASE / dioxygen activation / four-helix bundle / diiron / diferric-peroxo ligand
Function / homology:
Function and homology information
Biological speciesSulfurisphaera tokodaii str. 7 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsJeoung, J.-H. / Dobbek, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2008 390540038 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2026
Title: diFe-Sulerythin_E53D:E126D reduced
Authors: Jeoung, J.-H. / Runger, S. / Weisser, K. / Ruickoldt, J. / Bhattacharya, S. / Limberg, C. / Dobbek, H.
History
DepositionJul 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: diFe-Sulerythin_E53D:E126D reduced
B: diFe-Sulerythin_E53D:E126D reduced
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,66811
Polymers32,1402
Non-polymers5289
Water7,134396
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint-154 kcal/mol
Surface area12910 Å2
Unit cell
Length a, b, c (Å)72.558, 72.558, 98.888
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein diFe-Sulerythin_E53D:E126D reduced


Mass: 16070.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfurisphaera tokodaii str. 7 (archaea)
Production host: Escherichia coli B (bacteria)
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl
#4: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C7H17NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.34 Å3/Da / Density % sol: 47.39 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris pH 5.5 + 20-25% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.18→36.28 Å / Num. obs: 96602 / % possible obs: 99.8 % / Redundancy: 4.96 % / CC1/2: 1 / Net I/σ(I): 14.54
Reflection shellResolution: 1.18→1.25 Å / Num. unique obs: 15486 / CC1/2: 0.306

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.18→36.28 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1702 2101 2.18 %RANDOM
Rwork0.1442 ---
obs0.1448 96596 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.18→36.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2248 0 19 396 2663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072421
X-RAY DIFFRACTIONf_angle_d0.9143277
X-RAY DIFFRACTIONf_dihedral_angle_d14.667944
X-RAY DIFFRACTIONf_chiral_restr0.065334
X-RAY DIFFRACTIONf_plane_restr0.011436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.18-1.210.37881370.38166127X-RAY DIFFRACTION98
1.21-1.240.32071400.3116311X-RAY DIFFRACTION100
1.24-1.270.26761400.27466313X-RAY DIFFRACTION100
1.27-1.310.3131390.25196265X-RAY DIFFRACTION100
1.31-1.350.26571410.21856333X-RAY DIFFRACTION100
1.35-1.40.23031400.20276282X-RAY DIFFRACTION100
1.4-1.450.22791400.18296303X-RAY DIFFRACTION100
1.45-1.520.20661400.15846301X-RAY DIFFRACTION100
1.52-1.60.13811400.11836288X-RAY DIFFRACTION100
1.6-1.70.15411410.11396344X-RAY DIFFRACTION100
1.7-1.830.15591400.11536299X-RAY DIFFRACTION100
1.83-2.020.161400.12416332X-RAY DIFFRACTION100
2.02-2.310.14061400.12086291X-RAY DIFFRACTION100
2.31-2.910.15941410.13096354X-RAY DIFFRACTION100
2.91-36.280.15191420.13646352X-RAY DIFFRACTION99

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