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- PDB-8zn8: MjF-3C-CdS QDs -

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Basic information

Entry
Database: PDB / ID: 8zn8
TitleMjF-3C-CdS QDs
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / ferritin / quantum dots / Cds / catalysis / photosynthesis
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / intracellular iron ion homeostasis / cytoplasm
Similarity search - Function
Ferritin / 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
: / HYDROSULFURIC ACID / Ferritin
Similarity search - Component
Biological speciesPenaeus japonicus (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsDuan, M.P. / Zhang, T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Construction of an artificial photosynthesis system by incorporation of CdS quantum dots into the intrasubunit interface of a four-helix-bundle-structure enzyme
Authors: Duan, M.P. / Zhang, T.
History
DepositionMay 26, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,20778
Polymers115,4986
Non-polymers4,70972
Water9,548530
1
B: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules

B: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules

B: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules

B: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules

A: Ferritin
C: Ferritin
hetero molecules

A: Ferritin
C: Ferritin
hetero molecules

A: Ferritin
C: Ferritin
hetero molecules

A: Ferritin
C: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)480,828312
Polymers461,99224
Non-polymers18,836288
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_445x-1/2,y-1/2,z+1/21
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
crystal symmetry operation7_545-y+1/2,x-1/2,z+1/21
crystal symmetry operation8_455y-1/2,-x+1/2,z+1/21
Buried area107430 Å2
ΔGint-1524 kcal/mol
Surface area134410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.748, 126.748, 177.949
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11D-212-

MG

21B-301-

HOH

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Ferritin


Mass: 19249.656 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penaeus japonicus (crustacean) / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: T2B7E1, ferroxidase

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Non-polymers , 5 types, 602 molecules

#2: Chemical...
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: H2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.09 Å3/Da / Density % sol: 60.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 2.5 M NaCl, 100 mM MgCl2 and 100 mM Tris (pH 7.0)

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Data collection

DiffractionMean temperature: 300 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: May 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.25→44.81 Å / Num. obs: 129055 / % possible obs: 98 % / Redundancy: 1.34 % / CC1/2: 0.998 / Net I/σ(I): 14.4
Reflection shellResolution: 2.25→2.28 Å / Num. unique obs: 3530 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→44.81 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2074 6356 4.93 %
Rwork0.166 --
obs0.168 129055 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→44.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8094 0 100 530 8724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088283
X-RAY DIFFRACTIONf_angle_d0.81211156
X-RAY DIFFRACTIONf_dihedral_angle_d5.3341108
X-RAY DIFFRACTIONf_chiral_restr0.0431178
X-RAY DIFFRACTIONf_plane_restr0.0061469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.280.33742510.28983530X-RAY DIFFRACTION87
2.28-2.310.28622550.26764008X-RAY DIFFRACTION97
2.31-2.330.2696980.24224219X-RAY DIFFRACTION99
2.33-2.360.28371350.22334101X-RAY DIFFRACTION99
2.36-2.390.2731940.21854154X-RAY DIFFRACTION99
2.39-2.430.24542760.21834089X-RAY DIFFRACTION99
2.43-2.460.29362170.2054018X-RAY DIFFRACTION99
2.46-2.50.26831870.21364110X-RAY DIFFRACTION99
2.5-2.540.24471990.21014151X-RAY DIFFRACTION99
2.54-2.580.27662330.19814123X-RAY DIFFRACTION99
2.58-2.620.26932600.20294020X-RAY DIFFRACTION99
2.62-2.670.26841720.18744169X-RAY DIFFRACTION99
2.67-2.720.25023010.18923975X-RAY DIFFRACTION99
2.72-2.780.21222000.19914139X-RAY DIFFRACTION99
2.78-2.840.27881870.19014137X-RAY DIFFRACTION99
2.84-2.910.23831980.18414120X-RAY DIFFRACTION99
2.91-2.980.21971730.18544159X-RAY DIFFRACTION99
2.98-3.060.25452530.19014054X-RAY DIFFRACTION99
3.06-3.150.24842200.18654153X-RAY DIFFRACTION99
3.15-3.250.22382660.1694089X-RAY DIFFRACTION99
3.25-3.370.21482200.16424077X-RAY DIFFRACTION100
3.37-3.50.20361410.14764181X-RAY DIFFRACTION99
3.5-3.660.16022690.14684058X-RAY DIFFRACTION99
3.66-3.850.17622660.14014098X-RAY DIFFRACTION99
3.85-4.090.20551970.13254106X-RAY DIFFRACTION99
4.09-4.410.1621330.12744205X-RAY DIFFRACTION99
4.41-4.850.15531990.12254174X-RAY DIFFRACTION99
4.85-5.550.17062540.14874004X-RAY DIFFRACTION99
5.56-6.990.2062040.1764141X-RAY DIFFRACTION99
6.99-70.13371980.134137X-RAY DIFFRACTION99

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