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- PDB-7o9e: diNi-sulerythrin -

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Basic information

Entry
Database: PDB / ID: 7o9e
TitlediNi-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
NICKEL (II) ION / Sulerythrin
Similarity search - Component
Biological speciesSulfurisphaera tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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)32,9519
Polymers32,5872
Non-polymers3647
Water7,855436
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-132 kcal/mol
Surface area12760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.831, 72.831, 98.976
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-471-

HOH

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Components

#1: Protein Sulerythrin


Mass: 16293.276 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) (archaea)
Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7 / Gene: ST2370, STK_23700 / Production host: Escherichia coli B (bacteria) / References: UniProt: F9VPE5
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 47.42 %
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: 1.25→38.93 Å / Num. obs: 82488 / % possible obs: 99.74 % / Redundancy: 10.05 % / CC1/2: 1 / Net I/σ(I): 16.2
Reflection shellResolution: 1.25→1.29 Å / Num. unique obs: 8056 / CC1/2: 0.526

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J30

1j30


Resolution: 1.25→38.93 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.525 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15406 1074 1.3 %RANDOM
Rwork0.12516 ---
obs0.12555 81415 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.632 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0.1 Å20 Å2
2---0.21 Å2-0 Å2
3---0.68 Å2
Refinement stepCycle: 1 / Resolution: 1.25→38.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2254 0 7 436 2697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132448
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182274
X-RAY DIFFRACTIONr_angle_refined_deg1.8631.6533306
X-RAY DIFFRACTIONr_angle_other_deg1.7321.5865268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.225313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51922.553141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.215436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.771517
X-RAY DIFFRACTIONr_chiral_restr0.1130.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022880
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02586
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.941.3661219
X-RAY DIFFRACTIONr_mcbond_other1.8721.3571217
X-RAY DIFFRACTIONr_mcangle_it2.0952.0431543
X-RAY DIFFRACTIONr_mcangle_other2.0632.0431543
X-RAY DIFFRACTIONr_scbond_it3.311.6751229
X-RAY DIFFRACTIONr_scbond_other3.311.6791230
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6672.3851764
X-RAY DIFFRACTIONr_long_range_B_refined4.59419.3033247
X-RAY DIFFRACTIONr_long_range_B_other3.49917.6813082
X-RAY DIFFRACTIONr_rigid_bond_restr3.03134722
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.25→1.279 Å
RfactorNum. reflection% reflection
Rfree0.282 78 -
Rwork0.261 5856 -
obs--96.63 %

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