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- PDB-8fvv: Rubrerythrin from B. pseudomallei: iron-bound -

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Basic information

Entry
Database: PDB / ID: 8fvv
TitleRubrerythrin from B. pseudomallei: iron-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
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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: iron-bound
Authors: Monteiro, D.C.F. / Snell, M.E. / Budziszewski, G.R. / Bowman, S.E.J.
History
DepositionJan 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 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
C: Rubrerythrin
D: Rubrerythrin
E: Rubrerythrin
F: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,60218
Polymers111,9326
Non-polymers67012
Water14,412800
1
A: Rubrerythrin
B: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5346
Polymers37,3112
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-95 kcal/mol
Surface area12430 Å2
MethodPISA
2
C: Rubrerythrin
D: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5346
Polymers37,3112
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-96 kcal/mol
Surface area12410 Å2
MethodPISA
3
E: Rubrerythrin
F: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5346
Polymers37,3112
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-95 kcal/mol
Surface area12660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.170, 202.170, 69.825
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-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 800 / 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: 2.45 Å3/Da / Density % sol: 49.87 %
Crystal growTemperature: 273 K / Method: microbatch / pH: 6.75
Details: 0.15 M lithium sulfate 30% PEG 3350 0.1 M BTP pH 6.75 1 mM iron chloride

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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: Oct 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.93→29.9 Å / Num. obs: 61079 / % possible obs: 92.4 % / Observed criterion σ(I): 2 / Redundancy: 10.8 % / Biso Wilson estimate: 13.99 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.23 / Rpim(I) all: 0.073 / Rrim(I) all: 0.241 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) all% possible allRrim(I) all
1.93-2.0710.71.8981.535950.5970.60761.4
5.42-29.9110.06226.235940.9990.0191000.065

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
STARANISOdata scaling
MOLREP8FUHphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→29.9 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.281 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.159
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.209 2998 4.908 %RANDOM
Rwork0.161 58081 --
all0.163 ---
obs-61079 92.4 %-
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: 24.663 Å2
Baniso -1Baniso -2Baniso -3
1--0.013 Å2-0.006 Å20 Å2
2---0.013 Å2-0 Å2
3---0.042 Å2
Refinement stepCycle: LAST / Resolution: 1.93→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6464 0 12 800 7276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0126596
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165875
X-RAY DIFFRACTIONr_angle_refined_deg1.381.668905
X-RAY DIFFRACTIONr_angle_other_deg0.4791.57913524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0025828
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.339542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.019101048
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.48510353
X-RAY DIFFRACTIONr_chiral_restr0.0690.2918
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028046
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021594
X-RAY DIFFRACTIONr_nbd_refined0.230.21736
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.25459
X-RAY DIFFRACTIONr_nbtor_refined0.1880.23362
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.23530
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2660
X-RAY DIFFRACTIONr_metal_ion_refined0.10.218
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2080.29
X-RAY DIFFRACTIONr_nbd_other0.210.276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1430.224
X-RAY DIFFRACTIONr_mcbond_it2.0662.4963330
X-RAY DIFFRACTIONr_mcbond_other2.0662.4963330
X-RAY DIFFRACTIONr_mcangle_it3.1464.4684152
X-RAY DIFFRACTIONr_mcangle_other3.1474.4684153
X-RAY DIFFRACTIONr_scbond_it3.082.8423266
X-RAY DIFFRACTIONr_scbond_other3.082.8413265
X-RAY DIFFRACTIONr_scangle_it4.9125.0384753
X-RAY DIFFRACTIONr_scangle_other4.9125.0384754
X-RAY DIFFRACTIONr_lrange_it6.68825.7318340
X-RAY DIFFRACTIONr_lrange_other6.44124.1938081
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.931-1.9810.416200.306416X-RAY DIFFRACTION7.3524
1.981-2.0350.285710.2641564X-RAY DIFFRACTION28.639
2.035-2.0940.2551110.2342386X-RAY DIFFRACTION44.5973
2.094-2.1580.2531880.2312820X-RAY DIFFRACTION55.7037
2.158-2.2290.2571880.2143302X-RAY DIFFRACTION66.2868
2.229-2.3060.2742210.223673X-RAY DIFFRACTION77.4617
2.306-2.3930.2412160.1984153X-RAY DIFFRACTION88.6926
2.393-2.490.252050.1994307X-RAY DIFFRACTION95.4517
2.49-2.60.231790.1774332X-RAY DIFFRACTION100
2.6-2.7260.2131850.1614152X-RAY DIFFRACTION100
2.726-2.8720.2062050.1453894X-RAY DIFFRACTION100
2.872-3.0440.1912290.1543706X-RAY DIFFRACTION100
3.044-3.2520.2171550.1593488X-RAY DIFFRACTION100
3.252-3.5090.2171760.1543278X-RAY DIFFRACTION100
3.509-3.8390.1941390.1462992X-RAY DIFFRACTION100
3.839-4.2830.1831420.1222679X-RAY DIFFRACTION100
4.283-4.9290.1651210.1172395X-RAY DIFFRACTION100
4.929-5.9960.195990.1462042X-RAY DIFFRACTION100
5.996-8.3150.165950.1281578X-RAY DIFFRACTION100
8.315-29.90.151530.149924X-RAY DIFFRACTION99.8978

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