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- PDB-8fxd: Rubrerythrin from B. pseudomallei: manganese-bound -

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Basic information

Entry
Database: PDB / ID: 8fxd
TitleRubrerythrin from B. pseudomallei: manganese-bound
ComponentsRubrerythrin
KeywordsOXIDOREDUCTASE / metalloprotein / oxidative stress / non-heme
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
: / DI(HYDROXYETHYL)ETHER / Rubrerythrin
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsMonteiro, D.C.F. / Snell, M.E. / Budziszewski, G.R. / Bowman, S.E.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DBI1231306 United States
Other privateSkarlow Foundation
CitationJournal: To Be Published
Title: Rubrerythrin from B. pseudomallei: manganese-bound
Authors: Monteiro, D.C.F. / Snell, M.E. / Budziszewski, G.R. / Bowman, S.E.J.
History
DepositionJan 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: 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
M: Rubrerythrin
S: Rubrerythrin
Y: Rubrerythrin
5: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,33425
Polymers111,9326
Non-polymers1,40219
Water15,745874
1
A: Rubrerythrin
B: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8499
Polymers37,3112
Non-polymers5387
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6990 Å2
ΔGint-60 kcal/mol
Surface area12830 Å2
MethodPISA
2
M: Rubrerythrin
S: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6377
Polymers37,3112
Non-polymers3265
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-61 kcal/mol
Surface area12980 Å2
MethodPISA
3
Y: Rubrerythrin
5: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8499
Polymers37,3112
Non-polymers5387
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-57 kcal/mol
Surface area12820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.874, 201.874, 69.025
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Rubrerythrin /


Mass: 18655.389 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: BURPS1710b_A0924 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3JK21
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 874 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.42 Å3/Da / Density % sol: 49.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.138 M Li2SO4, 0.92 M BTP, pH 8, 22.08% PEG 3350, 0.8 mM MnCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.58→29.14 Å / Num. obs: 108953 / % possible obs: 93.7 % / Redundancy: 5.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.069 / Rrim(I) all: 0.115 / Net I/σ(I): 9.5
Reflection shellResolution: 1.58→1.692 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.833 / Num. unique obs: 5450 / CC1/2: 0.457 / Rpim(I) all: 0.807 / Rrim(I) all: 1.161 / % possible all: 59.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→29.14 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.824 / SU ML: 0.059 / Cross valid method: FREE R-VALUE / ESU R: 0.083 / ESU R Free: 0.083
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1755 5467 5.018 %
Rwork0.1477 103486 -
all0.149 --
obs-108953 93.7 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.178 Å2
Baniso -1Baniso -2Baniso -3
1-0.003 Å20.001 Å2-0 Å2
2--0.003 Å20 Å2
3----0.008 Å2
Refinement stepCycle: LAST / Resolution: 1.58→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6443 0 49 874 7366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0126706
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166002
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.669058
X-RAY DIFFRACTIONr_angle_other_deg0.5481.57913850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.575855
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.713543
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.738101076
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.93810360
X-RAY DIFFRACTIONr_chiral_restr0.0830.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028178
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021618
X-RAY DIFFRACTIONr_nbd_refined0.2320.21668
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1740.25282
X-RAY DIFFRACTIONr_nbtor_refined0.1880.23386
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.23495
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2660
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.380.27
X-RAY DIFFRACTIONr_nbd_other0.3430.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1230.232
X-RAY DIFFRACTIONr_mcbond_it1.8241.8053348
X-RAY DIFFRACTIONr_mcbond_other1.821.8043348
X-RAY DIFFRACTIONr_mcangle_it2.5333.2274185
X-RAY DIFFRACTIONr_mcangle_other2.5363.2274186
X-RAY DIFFRACTIONr_scbond_it3.6292.2553358
X-RAY DIFFRACTIONr_scbond_other3.6282.2563359
X-RAY DIFFRACTIONr_scangle_it5.8233.94859
X-RAY DIFFRACTIONr_scangle_other5.8223.9014860
X-RAY DIFFRACTIONr_lrange_it6.8219.4618353
X-RAY DIFFRACTIONr_lrange_other6.57818.0698059
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.620.306290.271333X-RAY DIFFRACTION3.4235
1.62-1.6650.2771350.2752453X-RAY DIFFRACTION24.959
1.665-1.7130.2932390.2544429X-RAY DIFFRACTION46.4616
1.713-1.7650.2562800.2295393X-RAY DIFFRACTION57.67
1.765-1.8230.2473430.2145966X-RAY DIFFRACTION66.6843
1.823-1.8870.2223440.1976545X-RAY DIFFRACTION75.4132
1.887-1.9580.2353590.197119X-RAY DIFFRACTION84.3732
1.958-2.0370.214230.1887582X-RAY DIFFRACTION93.7354
2.037-2.1270.1843720.1647744X-RAY DIFFRACTION99.6929
2.127-2.230.1753700.1497430X-RAY DIFFRACTION100
2.23-2.350.1674480.1376957X-RAY DIFFRACTION100
2.35-2.4920.1763660.1346687X-RAY DIFFRACTION100
2.492-2.6630.1723520.1286243X-RAY DIFFRACTION100
2.663-2.8740.1612690.1275889X-RAY DIFFRACTION100
2.874-3.1450.1682680.1425391X-RAY DIFFRACTION100
3.145-3.5110.172420.1434861X-RAY DIFFRACTION100
3.511-4.0450.1342160.1244336X-RAY DIFFRACTION100
4.045-4.930.1251710.1093666X-RAY DIFFRACTION100
4.93-6.8750.1691600.1472825X-RAY DIFFRACTION100
6.875-29.140.163810.1351640X-RAY DIFFRACTION100

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