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- PDB-7ek7: prawn ferritin to coordinate with heavy metal ions -

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Basic information

Entry
Database: PDB / ID: 7ek7
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: 2.7 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 4, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)117,13510
Polymers116,3326
Non-polymers8024
Water2,270126
1
C: Ferritin
F: Ferritin
A: Ferritin
B: Ferritin
hetero molecules

C: Ferritin
F: Ferritin
A: Ferritin
B: Ferritin
hetero molecules

C: Ferritin
F: Ferritin
A: Ferritin
B: Ferritin
hetero molecules

C: Ferritin
F: Ferritin
A: Ferritin
B: Ferritin
hetero molecules

D: Ferritin
E: Ferritin
hetero molecules

D: Ferritin
E: Ferritin
hetero molecules

D: Ferritin
E: Ferritin
hetero molecules

D: Ferritin
E: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)468,53840
Polymers465,32924
Non-polymers3,20916
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_554x+1/2,y+1/2,z-1/21
crystal symmetry operation6_444-x-1/2,-y-1/2,z-1/21
crystal symmetry operation7_454-y-1/2,x+1/2,z-1/21
crystal symmetry operation8_544y+1/2,-x-1/2,z-1/21
Buried area89880 Å2
ΔGint-572 kcal/mol
Surface area135950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.285, 126.285, 177.247
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein
Ferritin


Mass: 19388.699 Da / Num. of mol.: 6
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-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 3.04 Å3/Da / Density % sol: 59.5 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.5, 2.0 M Ammonium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.7→30.02 Å / Num. obs: 37909 / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.063 / Rrim(I) all: 0.166 / Χ2: 0.812 / Net I/σ(I): 3.8
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.7-2.86.70.65737970.7020.2740.7120.496
2.8-2.916.90.49537720.7980.2030.5350.537
2.91-3.047.20.40437460.8610.1620.4360.568
3.04-3.27.10.29637910.9110.120.320.657
3.2-3.46.80.2438030.9380.10.260.733
3.4-3.6670.20337700.9540.0830.220.93
3.66-4.037.20.15637850.9720.0630.1681.04
4.03-4.616.90.12537960.9790.0520.1351.047
4.61-5.87.10.1237910.9810.0480.1291.059
5.8-306.80.09138580.9930.0380.0991.036

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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: 2.7→30.02 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 35.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3362 2056 5.42 %
Rwork0.2535 35848 -
obs0.2579 37904 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 374.93 Å2 / Biso mean: 49.3934 Å2 / Biso min: 15.09 Å2
Refinement stepCycle: final / Resolution: 2.7→30.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8166 0 4 126 8296
Biso mean--202.02 39.67 -
Num. residues----1014
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.7-2.770.40851880.29232325
2.77-2.830.4268860.28152425
2.83-2.910.38831740.28842365
2.91-30.40461700.28592362
3-3.090.36021200.28652372
3.09-3.20.41821210.27052396
3.2-3.330.37291640.26442367
3.33-3.480.35541010.24962415
3.48-3.670.32161190.23532410
3.67-3.90.30071190.23612402
3.9-4.20.29281580.22552387
4.2-4.620.30361470.23322367
4.62-5.280.3141980.24272448
5.28-6.640.38221570.30092385
6.65-100.2861340.24072422

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