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- PDB-8sqt: Crystal Structure of Bacterioferritin (Bfr) from Brucella abortus... -

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Basic information

Entry
Database: PDB / ID: 8sqt
TitleCrystal Structure of Bacterioferritin (Bfr) from Brucella abortus (iron bound, cubic form 2, F16L mutant)
ComponentsBacterioferritin
KeywordsMETAL BINDING PROTEIN / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / heme binding / cytosol
Similarity search - Function
Bacterioferritin signature. / Bacterioferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / PROTOPORPHYRIN IX CONTAINING FE / Bacterioferritin
Similarity search - Component
Biological speciesBrucella abortus 2308 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of Bacterioferritin (Bfr) from Brucella abortus (iron bound, cubic form 2, F16L mutant)
Authors: Lovell, S. / Liu, L. / Battaile, K.P.
History
DepositionMay 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9039
Polymers18,8561
Non-polymers1,0478
Water52229
1
A: Bacterioferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)477,678216
Polymers452,54824
Non-polymers25,129192
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Buried area89590 Å2
ΔGint-1291 kcal/mol
Surface area134720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.718, 170.718, 170.718
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-202-

SO4

21A-203-

CL

31A-204-

CL

41A-208-

HEM

51A-208-

HEM

61A-317-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Bacterioferritin


Mass: 18856.180 Da / Num. of mol.: 1 / Mutation: F16L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus 2308 (bacteria) / Gene: bfr, BAB2_0675 / Plasmid: BrabA.00028.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2YKI4, ferroxidase

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Non-polymers , 5 types, 37 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.75 Å3/Da / Density % sol: 55.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Berkeley G7: 1.5M ammonium sulfate, 5% (v/v) MPD, 100 mM sodium acetate pH 4.5, BrabA.00028.a.A1.PW39164 at 10 mg/mL. Plate: 10390, well G7 drop 2. Puck: PSL-1812, Cryo: 2.5M lithium sulfate. ...Details: Berkeley G7: 1.5M ammonium sulfate, 5% (v/v) MPD, 100 mM sodium acetate pH 4.5, BrabA.00028.a.A1.PW39164 at 10 mg/mL. Plate: 10390, well G7 drop 2. Puck: PSL-1812, Cryo: 2.5M lithium sulfate. 10 minute soak in 25 mM ferrous ammonium sulfate in cryo
PH range: '

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Mar 14, 2022
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→49.28 Å / Num. obs: 11356 / % possible obs: 100 % / Redundancy: 38.8 % / CC1/2: 1 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.023 / Rrim(I) all: 0.143 / Χ2: 1.01 / Net I/σ(I): 26.3 / Num. measured all: 441158
Reflection shellResolution: 2.2→2.27 Å / % possible obs: 100 % / Redundancy: 41.5 % / Rmerge(I) obs: 2.706 / Num. measured all: 39929 / Num. unique obs: 962 / CC1/2: 0.693 / Rpim(I) all: 0.423 / Rrim(I) all: 2.74 / Χ2: 0.99 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4933: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→49.28 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2622 553 4.87 %
Rwork0.1937 --
obs0.1972 11345 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→49.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1291 0 58 29 1378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121371
X-RAY DIFFRACTIONf_angle_d1.071865
X-RAY DIFFRACTIONf_dihedral_angle_d16.122507
X-RAY DIFFRACTIONf_chiral_restr0.042191
X-RAY DIFFRACTIONf_plane_restr0.008240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.420.31121260.222618X-RAY DIFFRACTION100
2.42-2.770.27391430.24452629X-RAY DIFFRACTION100
2.77-3.490.3111350.22982677X-RAY DIFFRACTION100
3.49-49.280.23591490.16562868X-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)
15.2609-5.8722-2.05186.57721.94876.0417-0.26240.90610.19770.0983-0.10560.4418-0.5312-0.23560.36370.8796-0.14130.10860.81680.0460.899325.950249.176821.9283
22.4305-4.7751-3.50769.9536.58065.2245-0.073-0.0875-0.04210.01070.05170.1898-0.01910.20750.03620.3732-0.0965-0.08050.3610.03610.379835.190730.1746.2207
30.891-1.2515-0.8253.39192.08741.4681-0.0934-0.19620.09320.01790.1703-0.0706-0.05480.2227-0.11320.361-0.0703-0.03560.4376-0.02730.427941.767724.311211.7657
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 4 )
2X-RAY DIFFRACTION2chain 'A' and (resid 5 through 69 )
3X-RAY DIFFRACTION3chain 'A' and (resid 70 through 159 )

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