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- PDB-7ek5: prawn ferritin to coordinate with heavy metal ions -

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Basic information

Entry
Database: PDB / ID: 7ek5
Titleprawn ferritin to coordinate with heavy metal ions
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / heavy metal ion removal / prawn ferritin / cysteine / Hg
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / ferrous iron binding / intracellular iron ion homeostasis / cytoplasm
Similarity search - Function
Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMarsupenaeus japonicus (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWang, Y. / Zang, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)6214038 China
CitationJournal: Int J Mol Sci / Year: 2021
Title: Structural Insights for the Stronger Ability of Shrimp Ferritin to Coordinate with Heavy Metal Ions as Compared to Human H-Chain Ferritin.
Authors: Wang, Y. / Zang, J. / Wang, C. / Zhang, X. / Zhao, G.
History
DepositionApr 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)78,22812
Polymers77,5554
Non-polymers6738
Water00
1
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)469,36772
Polymers465,32924
Non-polymers4,03848
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
crystal symmetry operation10_554-y,-x,-z-1/21
crystal symmetry operation11_454-x+y-1,y,-z-1/21
crystal symmetry operation12_564x,x-y+1,-z-1/21
Buried area98650 Å2
ΔGint-892 kcal/mol
Surface area132750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.613, 155.613, 162.729
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein
Ferritin


Mass: 19388.699 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marsupenaeus japonicus (crustacean) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: T2B7E1, ferroxidase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
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: 3.67 Å3/Da / Density % sol: 66.46 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium acetate trihydrate pH 4.6, 2.0 M Sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3→30.02 Å / Num. obs: 23717 / % possible obs: 99.6 % / Redundancy: 10.4 % / CC1/2: 0.99 / Net I/σ(I): 8.7
Reflection shellResolution: 3→6.44 Å / Num. unique obs: 23717 / CC1/2: 0.961

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A4U

6a4u


Resolution: 3→30.02 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2235 1143 4.82 %
Rwork0.181 22571 -
obs0.1831 23714 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 183.86 Å2 / Biso mean: 37.5896 Å2 / Biso min: 14.47 Å2
Refinement stepCycle: final / Resolution: 3→30.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5444 0 7 0 5451
Biso mean--119.56 --
Num. residues----677
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.140.2831220.24662744286699
3.14-3.310.29811530.221927562909100
3.31-3.510.26781470.208827572904100
3.51-3.780.23131550.1927802935100
3.78-4.160.21491370.16727942931100
4.16-4.760.18741350.148128432978100
4.76-5.990.18181420.167928713013100
6-30.020.20711520.166430263178100

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