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- PDB-7ek4: prawn ferritin to coordinate with heavy metal ions -

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Basic information

Entry
Database: PDB / ID: 7ek4
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 / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / 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
Biological speciesMarsupenaeus japonicus (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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

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)117,87118
Polymers116,3326
Non-polymers1,53912
Water8,521473
1
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
hetero molecules

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

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

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

E: Ferritin
F: Ferritin
hetero molecules

E: Ferritin
F: Ferritin
hetero molecules

E: Ferritin
F: Ferritin
hetero molecules

E: Ferritin
F: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)471,48372
Polymers465,32924
Non-polymers6,15448
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
crystal symmetry operation5_445x-1/2,y-1/2,z+1/21
crystal symmetry operation6_445-x-1/2,-y-1/2,z+1/21
crystal symmetry operation7_445-y-1/2,x-1/2,z+1/21
crystal symmetry operation8_445y-1/2,-x-1/2,z+1/21
Buried area95350 Å2
ΔGint-1122 kcal/mol
Surface area132960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.372, 125.372, 176.189
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11C-369-

HOH

21D-366-

HOH

31F-376-

HOH

41F-377-

HOH

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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.: 6 / Source method: obtained synthetically / Formula: Hg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 2.98 Å3/Da / Density % sol: 58.67 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.5, 2.0 M Ammonium format

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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: 2.3→29.55 Å / Num. obs: 60408 / % possible obs: 99.8 % / Redundancy: 3.4 % / CC1/2: 0.982 / Rpim(I) all: 0.072 / Net I/σ(I): 5.8
Reflection shellResolution: 2.3→4.95 Å / Num. unique obs: 60408 / CC1/2: 0.982

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Processing

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

6a4u


Resolution: 2.3→29.55 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 22.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2369 3008 4.98 %
Rwork0.1949 57368 -
obs0.197 60376 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.12 Å2 / Biso mean: 31.1206 Å2 / Biso min: 14.36 Å2
Refinement stepCycle: final / Resolution: 2.3→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8130 0 12 473 8615
Biso mean--56.51 36.09 -
Num. residues----1014
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.330.26831140.20562751286599
2.33-2.370.2441670.201626892856100
2.37-2.420.25891640.195827072871100
2.42-2.460.27751650.202727172882100
2.46-2.510.23461270.198327482875100
2.51-2.570.21931340.184227152849100
2.57-2.630.2931000.196627662866100
2.63-2.690.24272010.187726662867100
2.69-2.770.2541210.20022740286199
2.77-2.850.24851380.197327652903100
2.85-2.940.27261530.197526842837100
2.94-3.040.23421270.201527672894100
3.04-3.170.23751180.197127262844100
3.17-3.310.23571660.200227252891100
3.31-3.480.21451320.192927592891100
3.48-3.70.24371560.188127092865100
3.7-3.990.22051150.176627602875100
3.99-4.390.20491260.186427542880100
4.39-5.020.22341590.184227612920100
5.02-6.310.24491660.228627072873100
6.32-29.550.23221590.19812752291199

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