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- PDB-8w8z: Escherichia coli ferritin mutant-M52H -

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Basic information

Entry
Database: PDB / ID: 8w8z
TitleEscherichia coli ferritin mutant-M52H
ComponentsBacterioferritin
KeywordsLYASE / IRON STORAGE
Function / homology
Function and homology information


: / ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / 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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsZhao, G. / Zeng, R.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31972018 China
CitationJournal: To Be Published
Title: Structure of Escherichia coli ferritin mutant M52H at 2.05 Angstroms resolution
Authors: Zhao, G. / Zeng, R.
History
DepositionSep 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 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: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
G: Bacterioferritin
H: Bacterioferritin


Theoretical massNumber of molelcules
Total (without water)146,2468
Polymers146,2468
Non-polymers00
Water1,02757
1
A: Bacterioferritin
B: Bacterioferritin
D: Bacterioferritin
G: Bacterioferritin

A: Bacterioferritin
B: Bacterioferritin
D: Bacterioferritin
G: Bacterioferritin

A: Bacterioferritin
B: Bacterioferritin
D: Bacterioferritin
G: Bacterioferritin

C: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
H: Bacterioferritin

C: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
H: Bacterioferritin

C: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
H: Bacterioferritin


Theoretical massNumber of molelcules
Total (without water)438,73724
Polymers438,73724
Non-polymers00
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation16_444x-1/2,-y-1/2,-z-1/21
crystal symmetry operation18_554z+1/2,-x+1/2,-y-1/21
crystal symmetry operation23_545y+1/2,-z-1/2,-x+1/21
Buried area73320 Å2
ΔGint-351 kcal/mol
Surface area137030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)224.990, 224.990, 224.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein
Bacterioferritin


Mass: 18280.727 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bfr / Production host: Escherichia coli (E. coli) / References: UniProt: A0A023L7J3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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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: 3.24 Å3/Da / Density % sol: 62.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 1.0 M NaCl, 5% PEG400, 100 mM HEPES/NaOH pH 7.5, and 20% Glycerol

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.05→37.5 Å / Num. obs: 230390 / % possible obs: 99.04 % / Redundancy: 2 % / CC1/2: 0.945 / Net I/σ(I): 34.03
Reflection shellResolution: 2.05→2.05 Å / Num. unique obs: 14354 / CC1/2: 0.702

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BFR

1bfr


Resolution: 2.05→37.5 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2515 3909 1.7 %
Rwork0.2189 --
obs0.2194 230390 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10264 0 0 57 10321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910424
X-RAY DIFFRACTIONf_angle_d1.04514040
X-RAY DIFFRACTIONf_dihedral_angle_d5.9061352
X-RAY DIFFRACTIONf_chiral_restr0.0751544
X-RAY DIFFRACTIONf_plane_restr0.0051824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.080.36181360.34827926X-RAY DIFFRACTION98
2.08-2.10.32841380.33198040X-RAY DIFFRACTION99
2.1-2.130.31971440.32198059X-RAY DIFFRACTION100
2.13-2.160.36821440.31558129X-RAY DIFFRACTION100
2.16-2.190.35341370.30078161X-RAY DIFFRACTION100
2.19-2.220.31221380.30177991X-RAY DIFFRACTION100
2.22-2.260.31081460.29378155X-RAY DIFFRACTION100
2.26-2.290.32321380.27668061X-RAY DIFFRACTION100
2.29-2.330.29661420.27088085X-RAY DIFFRACTION100
2.33-2.380.30671410.27368124X-RAY DIFFRACTION100
2.38-2.420.27361360.26668050X-RAY DIFFRACTION100
2.42-2.470.27611440.25128085X-RAY DIFFRACTION100
2.47-2.520.32121400.26568145X-RAY DIFFRACTION100
2.52-2.580.26671360.26048033X-RAY DIFFRACTION100
2.58-2.650.27841460.25018140X-RAY DIFFRACTION100
2.65-2.720.35151380.24548100X-RAY DIFFRACTION100
2.72-2.80.28241320.24588127X-RAY DIFFRACTION100
2.8-2.890.22671480.23178085X-RAY DIFFRACTION100
2.89-2.990.27391400.24478107X-RAY DIFFRACTION100
2.99-3.110.27041360.23958051X-RAY DIFFRACTION100
3.11-3.250.25521390.23698120X-RAY DIFFRACTION100
3.25-3.420.25781360.21518112X-RAY DIFFRACTION100
3.43-3.640.22871480.19488064X-RAY DIFFRACTION100
3.64-3.920.25881360.18438143X-RAY DIFFRACTION100
3.92-4.310.17361400.15758079X-RAY DIFFRACTION100
4.32-4.940.16321400.15288100X-RAY DIFFRACTION100
4.94-6.210.2381380.1938113X-RAY DIFFRACTION100
6.22-37.50.1941320.1538096X-RAY DIFFRACTION100

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