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- PDB-8w6q: ferritin from Ureaplasma diversum soaking in Fe2+ solution for 0 min -

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Basic information

Entry
Database: PDB / ID: 8w6q
Titleferritin from Ureaplasma diversum soaking in Fe2+ solution for 0 min
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / Ferritin / Fe-O cluster / 4-fold channel cavity / Ureaplasma diversum
Function / homology:
Function and homology information
Biological speciesUreaplasma diversum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.101 Å
AuthorsWang, W.M. / Xi, H.F. / Gong, W.J. / Ma, D.Y. / Wang, H.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)62075118, 21601112 China
CitationJournal: J Am Chem Soc / Year: 2024
Title: Growth Process of Fe-O Nanoclusters with Different Sizes Biosynthesized by Protein Nanocages.
Authors: Wenming Wang / Hongfang Xi / Dan Fu / Danyang Ma / Wenjun Gong / Yaqin Zhao / Xiaomei Li / Lijie Wu / Yu Guo / Guanghua Zhao / Hongfei Wang /
Abstract: All protein-directed syntheses of metal nanoclusters (NCs) and nanoparticles (NPs) have attracted considerable attention because protein scaffolds provide a unique metal coordination environment and ...All protein-directed syntheses of metal nanoclusters (NCs) and nanoparticles (NPs) have attracted considerable attention because protein scaffolds provide a unique metal coordination environment and can adjust the shape and morphology of NCs and NPs. However, the detailed formation mechanisms of NCs or NPs directed by protein templates remain unclear. In this study, by taking advantage of the ferritin nanocage as a biotemplate to monitor the growth of Fe-O NCs as a function of time, we synthesized a series of iron NCs with different sizes and shapes and subsequently solved their corresponding three-dimensional atomic-scale structures by X-ray protein crystallography and cryo-electron microscopy. The time-dependent structure analyses revealed the growth process of these Fe-O NCs with the 4-fold channel of ferritin as nucleation sites. To our knowledge, the newly biosynthesized FeOGlu represents the largest Fe-O NCs with a definite atomic structure. This study contributes to our understanding of the formation mechanism of iron NCs and provides an effective method for metal NC synthesis.
History
DepositionAug 29, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,20819
Polymers21,2551
Non-polymers95318
Water2,288127
1
A: Ferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)532,999456
Polymers510,12024
Non-polymers22,879432
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_665-y+1,-z+1,x1
crystal symmetry operation13_556y,x,-z+11
crystal symmetry operation14_666-y+1,-x+1,-z+11
crystal symmetry operation15_565y,-x+1,z1
crystal symmetry operation16_655-y+1,x,z1
crystal symmetry operation17_556x,z,-y+11
crystal symmetry operation18_655-x+1,z,y1
crystal symmetry operation19_666-x+1,-z+1,-y+11
crystal symmetry operation20_565x,-z+1,y1
crystal symmetry operation21_556z,y,-x+11
crystal symmetry operation22_565z,-y+1,x1
crystal symmetry operation23_655-z+1,y,x1
crystal symmetry operation24_666-z+1,-y+1,-x+11
Buried area89870 Å2
ΔGint-575 kcal/mol
Surface area157810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.814, 179.814, 179.814
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-203-

FE

21A-378-

HOH

31A-416-

HOH

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Components

#1: Protein Ferritin


Mass: 21254.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: WP_081847832.1 / Source: (gene. exp.) Ureaplasma diversum (bacteria) / Gene: UDIV_5880 / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.85 Å3/Da / Density % sol: 56.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Bicine, MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1.55 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.55 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 27415 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.026 / Rrim(I) all: 0.212 / Χ2: 1.395 / Net I/σ(I): 3.3
Reflection shell

Diffraction-ID: 1 / Redundancy: 15 % / % possible all: 100

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2
2.1-2.141.5587150.8210.950.2240.990.512
2.14-2.181.3567410.8740.9660.1810.990.554
2.18-2.221.2897430.910.9760.1660.990.574
2.22-2.261.227220.950.9870.1470.990.595
2.26-2.311.0417610.9470.9860.1240.990.684
2.31-2.370.9567260.9490.9870.1140.9630.708
2.37-2.420.8337220.9730.9930.1010.8390.755
2.42-2.490.7267490.9740.9940.0870.7310.848
2.49-2.560.6337390.9820.9950.0750.6380.984
2.56-2.650.5427480.9830.9960.0650.5461.06
2.65-2.740.4857320.9920.9980.0560.4881.165
2.74-2.850.4057500.9920.9980.0470.4081.384
2.85-2.980.3557500.9950.9990.0430.3581.594
2.98-3.140.297470.9940.9990.0350.2921.871
3.14-3.330.247660.9960.9990.030.2412.151
3.33-3.590.197540.9980.9990.0230.1922.429
3.59-3.950.1627770.99810.020.1642.706
3.95-4.520.1367770.99910.0170.1372.751
4.52-5.70.1197980.99810.0140.1192.131
5.7-100.0878820.9980.9990.0110.0881.631

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.101→44.954 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2254 2743 10.01 %
Rwork0.1787 --
obs0.1832 27415 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.101→44.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1421 0 18 127 1566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061488
X-RAY DIFFRACTIONf_angle_d0.7962012
X-RAY DIFFRACTIONf_dihedral_angle_d6.6881596
X-RAY DIFFRACTIONf_chiral_restr0.047216
X-RAY DIFFRACTIONf_plane_restr0.004261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.101-2.13680.31281390.24021225X-RAY DIFFRACTION100
2.1368-2.17560.26061400.21681221X-RAY DIFFRACTION100
2.1756-2.21750.25481400.21591252X-RAY DIFFRACTION100
2.2175-2.26270.22161340.19471215X-RAY DIFFRACTION100
2.2627-2.31190.24581410.19121262X-RAY DIFFRACTION100
2.3119-2.36570.24551330.21531220X-RAY DIFFRACTION100
2.3657-2.42480.29381390.21011235X-RAY DIFFRACTION100
2.4248-2.49040.271350.20911226X-RAY DIFFRACTION100
2.4904-2.56370.26581410.22521232X-RAY DIFFRACTION100
2.5637-2.64640.22321330.20661238X-RAY DIFFRACTION100
2.6464-2.7410.32561330.22361229X-RAY DIFFRACTION100
2.741-2.85070.30991360.2131248X-RAY DIFFRACTION100
2.8507-2.98040.26271390.21341219X-RAY DIFFRACTION100
2.9804-3.13750.21141360.19881222X-RAY DIFFRACTION100
3.1375-3.33410.26921330.18691257X-RAY DIFFRACTION100
3.3341-3.59140.20971340.16171234X-RAY DIFFRACTION100
3.5914-3.95260.20671330.14251242X-RAY DIFFRACTION100
3.9526-4.52410.17891380.13361234X-RAY DIFFRACTION100
4.5241-5.69810.17231420.15011233X-RAY DIFFRACTION100
5.6981-44.9540.20921440.18881228X-RAY DIFFRACTION98

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