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

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Basic information

Entry
Database: PDB / ID: 8sqq
TitleCrystal Structure of Bacterioferritin (Bfr) from Brucella abortus (Apo 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
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: 2.25 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 (Apo 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)19,7366
Polymers18,8561
Non-polymers8805
Water52229
1
A: Bacterioferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)473,657144
Polymers452,54824
Non-polymers21,108120
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 area85740 Å2
ΔGint-1141 kcal/mol
Surface area136720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.516, 171.516, 171.516
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-201-

CL

21A-202-

CL

31A-204-

SO4

41A-205-

HEM

51A-205-

HEM

61A-306-

HOH

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Components

#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
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.79 Å3/Da / Density % sol: 55.87 %
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-1810, Cryo: 2.5M lithium sulfate
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: 2.25→42.88 Å / Num. obs: 10780 / % possible obs: 100 % / Redundancy: 38.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.206 / Rpim(I) all: 0.033 / Rrim(I) all: 0.209 / Χ2: 1 / Net I/σ(I): 18.1 / Num. measured all: 419133
Reflection shellResolution: 2.25→2.32 Å / % possible obs: 100 % / Redundancy: 41.2 % / Rmerge(I) obs: 2.857 / Num. measured all: 39593 / Num. unique obs: 961 / CC1/2: 0.668 / Rpim(I) all: 0.448 / Rrim(I) all: 2.892 / Χ2: 1 / 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: 2.25→39.35 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2455 520 4.83 %
Rwork0.189 --
obs0.1917 10773 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→39.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1294 0 55 29 1378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131374
X-RAY DIFFRACTIONf_angle_d1.1391868
X-RAY DIFFRACTIONf_dihedral_angle_d16.631510
X-RAY DIFFRACTIONf_chiral_restr0.045191
X-RAY DIFFRACTIONf_plane_restr0.011240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.480.29371340.22042477X-RAY DIFFRACTION100
2.48-2.840.28831260.2352496X-RAY DIFFRACTION100
2.84-3.570.26261330.21632556X-RAY DIFFRACTION100
3.57-39.350.21831270.16042724X-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)
12.4187-3.6997-2.37525.70173.89873.6382-0.1896-0.1968-0.1243-0.05390.13860.4494-0.07740.22850.11980.3608-0.1139-0.07450.35640.0430.42832.518330.82676.6633
20.9994-1.8343-1.37623.40192.70572.43870.0415-0.13630.19570.06250.0742-0.1146-0.16650.194-0.13080.3373-0.0854-0.04620.48-0.03210.450741.702126.584815.065
31.92440.77312.19576.24232.88073.5457-0.28710.05880.1247-0.05940.0295-0.0722-0.0982-0.1670.21460.2391-0.03340.01590.3990.02370.388944.39686.698-2.1382
42.415-2.1894-2.59934.40242.59463.4203-0.2139-0.39330.0933-0.05480.18240.3402-0.29570.53540.00780.3415-0.0793-0.05290.4345-0.02030.516937.369833.55787.3231
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 74 )
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 144 )
3X-RAY DIFFRACTION3chain 'A' and (resid 145 through 159 )
4X-RAY DIFFRACTION4chain 'A' and (resid 0 through 35 )

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