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

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Basic information

Entry
Database: PDB / ID: 8sqp
TitleCrystal Structure of Bacterioferritin (Bfr) from Brucella abortus (Apo, 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: 2.05 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, 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)19,6196
Polymers18,8561
Non-polymers7635
Water54030
1
A: Bacterioferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)470,858144
Polymers452,54824
Non-polymers18,310120
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 area79110 Å2
ΔGint-746 kcal/mol
Surface area138280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.069, 112.069, 112.069
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432
Components on special symmetry positions
IDModelComponents
11A-201-

CL

21A-202-

CL

31A-204-

CA

41A-205-

HEM

51A-205-

HEM

61A-307-

HOH

71A-329-

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


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.11 Å3/Da / Density % sol: 60.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Berkeley screen condition H3: 20% (w/v) PEG 3350, 100 mM Calcium chloride. BrabA.00028.a.A1.PW39164 at 10 mg/mL. Plate: 13090, well C3 drop 2. Puck: PSL-1806, Cryo: 30% PEG 3350 + crystallant
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: 2.05→45.75 Å / Num. obs: 15708 / % possible obs: 100 % / Redundancy: 39.2 % / CC1/2: 1 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.016 / Rrim(I) all: 0.102 / Χ2: 1 / Net I/σ(I): 28.2 / Num. measured all: 615703
Reflection shellResolution: 2.05→2.11 Å / % possible obs: 100 % / Redundancy: 41.8 % / Rmerge(I) obs: 3.359 / Num. measured all: 49707 / Num. unique obs: 1190 / CC1/2: 0.661 / Rpim(I) all: 0.523 / Rrim(I) all: 3.4 / Χ2: 0.97 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4933: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→31.08 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.27 / Phase error: 24.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.215 812 5.17 %
Rwork0.1957 --
obs0.1967 15694 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→31.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1277 0 47 30 1354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031348
X-RAY DIFFRACTIONf_angle_d0.5511830
X-RAY DIFFRACTIONf_dihedral_angle_d14.472501
X-RAY DIFFRACTIONf_chiral_restr0.029189
X-RAY DIFFRACTIONf_plane_restr0.003235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.180.29371200.25132410X-RAY DIFFRACTION100
2.18-2.350.23981310.22172433X-RAY DIFFRACTION100
2.35-2.580.22831510.20562409X-RAY DIFFRACTION100
2.58-2.960.25071370.22632456X-RAY DIFFRACTION100
2.96-3.720.2211340.20962499X-RAY DIFFRACTION100
3.73-31.080.19121390.17292675X-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)
12.6165-1.8289-2.03588.02584.48097.13280.0609-0.14090.16980.0280.0665-0.1391-0.10640.1403-0.06120.3202-0.0262-0.02360.36360.01820.407238.016632.73876.4494
22.4603-3.4691-1.458.46074.19953.63-0.2085-0.29010.0345-0.11010.13020.5628-0.0796-0.0170.11890.4033-0.0221-0.01970.41250.00820.483532.367130.77756.6355
34.48520.65130.20782.56032.90483.3596-0.1857-0.00190.83851.2873-0.8215-0.898-1.59210.96610.55610.9561-0.1792-0.04730.7193-0.02910.625849.487726.60810.2775
44.7577-4.0029-3.66566.10855.30876.2168-0.2414-0.45680.2050.1960.2779-0.10040.04790.384-0.24820.4643-0.05590.00540.4874-0.02140.475742.157930.607817.0052
55.9282-5.9829-3.93245.91364.02192.9008-0.4883-0.4139-0.14840.64420.32680.51440.35960.01080.11290.5326-0.02710.01740.5037-0.02920.491838.878722.415916.5854
61.55810.37591.47134.13340.94796.4175-0.01190.07180.0770.3302-0.0246-0.1821-0.0059-0.26350.22090.44870.02840.06110.49040.01180.413543.25976.7907-2.4313
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 35 )
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 74 )
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 82 )
4X-RAY DIFFRACTION4chain 'A' and (resid 83 through 113 )
5X-RAY DIFFRACTION5chain 'A' and (resid 114 through 144 )
6X-RAY DIFFRACTION6chain 'A' and (resid 145 through 160 )

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