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- PDB-7o90: Mono-Fe-sulerythrin -

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Basic information

Entry
Database: PDB / ID: 7o90
TitleMono-Fe-sulerythrin
ComponentsSulerythrin
KeywordsOXIDOREDUCTASE / sulerythrin / Hydrogen peroxide / molecular oxygen / bi-metallic binding site
Function / homology
Function and homology information


oxidoreductase activity / metal ion binding
Similarity search - Function
Rubrerythrin, diiron-binding domain / Rubrerythrin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
Biological speciesSulfurisphaera tokodaii str. 7 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsJeoung, J.-H. / Dobbek, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)390540038 Germany
CitationJournal: Inorg.Chem. / Year: 2021
Title: Bimetallic Mn, Fe, Co, and Ni Sites in a Four-Helix Bundle Protein: Metal Binding, Structure, and Peroxide Activation.
Authors: Jeoung, J.H. / Runger, S. / Haumann, M. / Neumann, B. / Klemke, F. / Davis, V. / Fischer, A. / Dau, H. / Wollenberger, U. / Dobbek, H.
History
DepositionApr 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulerythrin
B: Sulerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3796
Polymers32,1962
Non-polymers1834
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-103 kcal/mol
Surface area12630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.877, 72.877, 98.322
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-330-

HOH

21A-446-

HOH

31A-456-

HOH

41B-429-

HOH

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Components

#1: Protein Sulerythrin


Mass: 16098.076 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) / References: UniProt: F9VPE5
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 47.46 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris (pH 5.5) and 20-25% (w/v) PEG3350

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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: Nov 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.49→49.16 Å / Num. obs: 48401 / % possible obs: 99.98 % / Redundancy: 10.29 % / CC1/2: 0.999 / Net I/σ(I): 13.7
Reflection shellResolution: 1.49→1.54 Å / Num. unique obs: 4793 / CC1/2: 0.661

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J30

1j30


Resolution: 1.49→49.16 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1778 2101 4.34 %
Rwork0.1496 --
obs0.1509 48393 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.49→49.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2223 0 4 292 2519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082332
X-RAY DIFFRACTIONf_angle_d0.9073144
X-RAY DIFFRACTIONf_dihedral_angle_d12.814878
X-RAY DIFFRACTIONf_chiral_restr0.058320
X-RAY DIFFRACTIONf_plane_restr0.009420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.520.27291390.26193055X-RAY DIFFRACTION100
1.52-1.560.28031390.2413056X-RAY DIFFRACTION100
1.56-1.60.23191400.21063092X-RAY DIFFRACTION100
1.6-1.650.21781410.19583098X-RAY DIFFRACTION100
1.65-1.70.21111390.18243069X-RAY DIFFRACTION100
1.7-1.760.22171380.17953053X-RAY DIFFRACTION100
1.76-1.840.18891410.17823101X-RAY DIFFRACTION100
1.84-1.920.17961400.16113082X-RAY DIFFRACTION100
1.92-2.020.15281390.14453074X-RAY DIFFRACTION100
2.02-2.150.18081410.13443113X-RAY DIFFRACTION100
2.15-2.310.14421390.13043057X-RAY DIFFRACTION100
2.31-2.550.15211410.13333105X-RAY DIFFRACTION100
2.55-2.910.16351410.14093108X-RAY DIFFRACTION100
2.91-3.670.1771400.14783091X-RAY DIFFRACTION100
3.67-49.160.17521430.13423138X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.3458-0.1088-0.74091.5646-0.12631.5002-0.03390.1451-0.2190.1791-0.0056-0.30450.11960.11430.02780.20540.0215-0.06370.16550.03470.188213.698527.925630.1511
25.46220.3202-1.86571.7133-0.14461.72230.0639-0.30960.0670.256-0.0012-0.1775-0.0990.0419-0.07830.2013-0.0073-0.05560.19650.02130.137810.521735.936132.4436
31.46671.1319-0.10852.5615-0.02090.6731-0.04530.0786-0.2915-0.19320.0426-0.40350.03940.07160.00510.18330.01810.03780.1892-0.01810.281714.371322.734913.3529
43.19932.9438-1.59477.6953-3.12183.4293-0.05770.2859-0.0715-0.43120.2034-0.0279-0.0622-0.0705-0.18030.16960.01760.02480.1535-0.04990.14385.860826.03598.9204
51.15741.0073-0.09147.3028-1.43480.98270.0403-0.0885-0.26140.2104-0.0527-0.34020.07090.04110.04610.1460.0206-0.02040.15520.00430.177410.689725.353521.7623
61.16860.18220.06741.774-0.04890.63580.0412-0.2245-0.2350.3036-0.0264-0.17350.02230.017-0.04010.1557-0.0008-0.03080.15360.03190.1416.136326.241828.7769
74.2883-0.449-0.99762.19460.07022.76490.0425-0.51920.03870.53010.0099-0.48770.00650.26270.00510.358-0.0061-0.18240.33540.05720.256319.872231.950940.6105
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 37 )
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 66 )
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 112 )
4X-RAY DIFFRACTION4chain 'A' and (resid 113 through 143 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 37 )
6X-RAY DIFFRACTION6chain 'B' and (resid 38 through 97 )
7X-RAY DIFFRACTION7chain 'B' and (resid 98 through 142 )

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