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- PDB-9fj2: Rubrerythrin from Clostridium difficile P28 -

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Basic information

Entry
Database: PDB / ID: 9fj2
TitleRubrerythrin from Clostridium difficile P28
ComponentsRubrerythrin
KeywordsOXIDOREDUCTASE / Non-heme iron / Iron-Cysteine center / Dinuclear / Rubredoxin domain
Function / homology
Function and homology information


oxidoreductase activity / iron ion binding
Similarity search - Function
: / : / Rubrerythrin, rubredoxin-like domain / Rubrerythrin, diiron-binding domain / Rubrerythrin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / OXYGEN ATOM / Rubrerythrin
Similarity search - Component
Biological speciesClostridioides difficile P28 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsSalgueiro, B.A. / Matias, P.M. / Romao, C.V.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Foundation for Science and Technology (FCT) Portugal
CitationJournal: To Be Published
Title: The X-ray crystal structure of the Rubrerythrin from Clostridium difficile P28 obtain by microdialysis method.
Authors: Salgueiro, B.A. / Matias, P.M. / Romao, C.V.
History
DepositionMay 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 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: Rubrerythrin
B: Rubrerythrin
C: Rubrerythrin
D: Rubrerythrin
E: Rubrerythrin
F: Rubrerythrin
G: Rubrerythrin
H: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,83537
Polymers163,4148
Non-polymers1,42029
Water8,503472
1
A: Rubrerythrin
B: Rubrerythrin
C: Rubrerythrin
D: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,42519
Polymers81,7074
Non-polymers71815
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21800 Å2
ΔGint-216 kcal/mol
Surface area29380 Å2
MethodPISA
2
E: Rubrerythrin
F: Rubrerythrin
G: Rubrerythrin
H: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,40918
Polymers81,7074
Non-polymers70214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21780 Å2
ΔGint-222 kcal/mol
Surface area29980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.767, 67.674, 95.325
Angle α, β, γ (deg.)93.290, 98.337, 106.878
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Rubrerythrin


Mass: 20426.812 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile P28 (bacteria)
Gene: CIAN88_10840, DXA38_08075, G4D54_07625, I5Q87_04165
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A099I6D2
#2: Chemical...
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / 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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 298.15 K / Method: microdialysis / pH: 8 / Details: 2.5M Ammonium Sulfate in 0.1M Tris HCl pH8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.19→50.66 Å / Num. obs: 71248 / % possible obs: 94.3 % / Redundancy: 3.46 % / Biso Wilson estimate: 28.59 Å2 / CC1/2: 0.949 / Rmerge(I) obs: 0.292 / Rpim(I) all: 0.182 / Rrim(I) all: 0.345 / Net I/σ(I): 2.1
Reflection shellResolution: 2.19→2.232 Å / Rmerge(I) obs: 1.715 / Num. unique obs: 3618 / CC1/2: 0.442 / Rpim(I) all: 1.062 / Rrim(I) all: 2.02

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Processing

Software
NameVersionClassification
autoPROC1.0.5data processing
PHENIX1.18.2_3874refinement
Aimlessv0.7.15data scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→36.15 Å / SU ML: 0.3808 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 34.3447
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3206 3466 4.88 %
Rwork0.2636 67507 -
obs0.2663 70973 93.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.81 Å2
Refinement stepCycle: LAST / Resolution: 2.19→36.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11296 0 29 472 11797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002411536
X-RAY DIFFRACTIONf_angle_d0.488715558
X-RAY DIFFRACTIONf_chiral_restr0.03391624
X-RAY DIFFRACTIONf_plane_restr0.00282046
X-RAY DIFFRACTIONf_dihedral_angle_d6.15211509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.220.37561550.31392706X-RAY DIFFRACTION92.83
2.22-2.260.37491320.30242676X-RAY DIFFRACTION92.8
2.26-2.290.33061380.29422650X-RAY DIFFRACTION93.03
2.29-2.330.32931270.2892685X-RAY DIFFRACTION92.65
2.33-2.360.33371230.29142672X-RAY DIFFRACTION93.2
2.36-2.40.40481280.29672715X-RAY DIFFRACTION93.8
2.4-2.450.33671610.29542664X-RAY DIFFRACTION93.57
2.45-2.50.32091330.28762723X-RAY DIFFRACTION93.61
2.5-2.550.34241290.2992636X-RAY DIFFRACTION92.94
2.55-2.60.33511710.29382736X-RAY DIFFRACTION94.05
2.6-2.660.3591320.29632638X-RAY DIFFRACTION93.96
2.66-2.730.33651520.28372712X-RAY DIFFRACTION93.56
2.73-2.80.35411330.28542654X-RAY DIFFRACTION93.3
2.8-2.890.34721340.28472721X-RAY DIFFRACTION93.45
2.89-2.980.30481620.26742673X-RAY DIFFRACTION93.72
2.98-3.080.34311280.27362747X-RAY DIFFRACTION95.74
3.08-3.210.32331400.25652726X-RAY DIFFRACTION95.34
3.21-3.350.34351450.26322747X-RAY DIFFRACTION95.57
3.35-3.530.32361360.24612762X-RAY DIFFRACTION95.14
3.53-3.750.27511370.23852730X-RAY DIFFRACTION94.93
3.75-4.040.2891380.23352715X-RAY DIFFRACTION94.85
4.04-4.450.27771300.22392721X-RAY DIFFRACTION94.44
4.45-5.090.28981140.23422722X-RAY DIFFRACTION93.78
5.09-6.410.33231380.28132686X-RAY DIFFRACTION93.79
6.41-36.150.30621500.25572690X-RAY DIFFRACTION93.76
Refinement TLS params.Method: refined / Origin x: -17.1154285304 Å / Origin y: 2.5491215139 Å / Origin z: -30.2770043181 Å
111213212223313233
T0.158606443974 Å20.0147282842052 Å20.0271536998127 Å2-0.184847808537 Å20.0180090322282 Å2--0.22299947877 Å2
L0.213276264058 °20.0033548943781 °20.0795206470442 °2-0.109198948597 °20.0441821432349 °2--0.187132816313 °2
S-0.0163698081101 Å °-0.0112364612256 Å °-0.0230643542852 Å °-0.0196125019271 Å °0.00157306016197 Å °0.00140973227154 Å °-0.020172638761 Å °-0.00613614193899 Å °0.0153602702749 Å °
Refinement TLS groupSelection details: all

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