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- PDB-7dqo: Marsupenaeus japonicus ferritin mutant-D132R -

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Basic information

Entry
Database: PDB / ID: 7dqo
TitleMarsupenaeus japonicus ferritin mutant-D132R
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / iron / catalysis / nanocage
Function / homology
Function and homology information


ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / cytosol
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 speciesPenaeus japonicus (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 Å
AuthorsTan, X. / Liu, Y. / Zang, J. / Zhang, T. / Zhao, G.
Funding support1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31730069
CitationJournal: Int.J.Biol.Macromol. / Year: 2021
Title: Hyperthermostability of prawn ferritin nanocage facilitates its application as a robust nanovehicle for nutraceuticals.
Authors: Tan, X. / Liu, Y. / Zang, J. / Zhang, T. / Zhao, G.
History
DepositionDec 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 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
G: Ferritin
H: Ferritin
I: Ferritin
J: Ferritin
K: Ferritin
L: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,49124
Polymers232,82112
Non-polymers67012
Water19,2581069
1
A: Ferritin
C: Ferritin
F: Ferritin
H: Ferritin
hetero molecules

A: Ferritin
C: Ferritin
F: Ferritin
H: Ferritin
hetero molecules

A: Ferritin
C: Ferritin
F: Ferritin
H: Ferritin
hetero molecules

A: Ferritin
C: Ferritin
F: Ferritin
H: Ferritin
hetero molecules

J: Ferritin
L: Ferritin
hetero molecules

J: Ferritin
L: Ferritin
hetero molecules

J: Ferritin
L: Ferritin
hetero molecules

J: Ferritin
L: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)466,98248
Polymers465,64224
Non-polymers1,34024
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 operation1_556x,y,z+11
crystal symmetry operation2_556-x,-y,z+11
crystal symmetry operation3_556-y,x,z+11
crystal symmetry operation4_556y,-x,z+11
Buried area93800 Å2
ΔGint-624 kcal/mol
Surface area131720 Å2
MethodPISA
2
B: Ferritin
D: Ferritin
E: Ferritin
G: Ferritin
I: Ferritin
K: Ferritin
hetero molecules

B: Ferritin
D: Ferritin
E: Ferritin
G: Ferritin
I: Ferritin
K: Ferritin
hetero molecules

B: Ferritin
D: Ferritin
E: Ferritin
G: Ferritin
I: Ferritin
K: Ferritin
hetero molecules

B: Ferritin
D: Ferritin
E: Ferritin
G: Ferritin
I: Ferritin
K: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)466,98248
Polymers465,64224
Non-polymers1,34024
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
Buried area93900 Å2
ΔGint-634 kcal/mol
Surface area130860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.448, 125.448, 176.178
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4
Components on special symmetry positions
IDModelComponents
11E-365-

HOH

21F-394-

HOH

31I-1122-

HOH

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Components

#1: Protein
Ferritin


Mass: 19401.740 Da / Num. of mol.: 12 / Mutation: D132R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penaeus japonicus (crustacean) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: T2B7E1, ferroxidase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1069 / 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: 58.68 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris-HCl (pH 8.5), 30% v/v 2-Propanol

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Data collection

DiffractionMean temperature: 273.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.06
ReflectionResolution: 1.7→29.9821 Å / Num. obs: 297165 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.98 / Net I/σ(I): 22.77
Reflection shellResolution: 1.7→1.73 Å / CC1/2: 0.98

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A4U

6a4u


Resolution: 1.701→29.982 Å / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.92 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2756 2015 0.68 %
Rwork0.2401 294738 -
obs0.2408 297165 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.61 Å2 / Biso mean: 20.8305 Å2 / Biso min: 6.75 Å2
Refinement stepCycle: final / Resolution: 1.701→29.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16344 0 12 1069 17425
Biso mean--58.97 20.15 -
Num. residues----2028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716632
X-RAY DIFFRACTIONf_angle_d0.81722368
X-RAY DIFFRACTIONf_chiral_restr0.0422352
X-RAY DIFFRACTIONf_plane_restr0.0042964
X-RAY DIFFRACTIONf_dihedral_angle_d18.43110164
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7012-1.74370.37171440.32782101321157
1.7437-1.79090.37471410.32232099421135
1.7909-1.84350.28071450.29852096721112
1.8435-1.9030.3361420.2842102421166
1.903-1.9710.3321400.27412100421144
1.971-2.04980.31321410.26212103021171
2.0498-2.1430.30821460.25312104221188
2.143-2.25580.2641440.25082099521139
2.2558-2.39690.29821440.252106921213
2.3969-2.58170.27121450.24632103821183
2.5817-2.84080.28041440.2342108521229
2.8408-3.25040.24091460.22672106721213
3.2504-4.08960.22741460.20512115121297
4.0896-20.17330.26331460.2072125921405

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