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- PDB-7cpi: His-Mediated Reversible Self-assembly of Ferritin Nanocage with Z... -

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Basic information

Entry
Database: PDB / ID: 7cpi
TitleHis-Mediated Reversible Self-assembly of Ferritin Nanocage with Zn binding
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / Ferritin / Assembly / Zn binding
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 speciesPenaeus japonicus (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.602 Å
AuthorsGu, C. / Zhang, T. / Zhao, G.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31730069 China
National Natural Science Foundation of China (NSFC)31972018 China
CitationJournal: Acs Nano / Year: 2020
Title: His-Mediated Reversible Self-Assembly of Ferritin Nanocages through Two Different Switches for Encapsulation of Cargo Molecules.
Authors: Gu, C. / Zhang, T. / Lv, C. / Liu, Y. / Wang, Y. / Zhao, G.
History
DepositionAug 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)119,53825
Polymers118,4106
Non-polymers1,12819
Water28816
1
A: Ferritin
B: Ferritin
F: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
F: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
F: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
F: Ferritin
hetero molecules

E: Ferritin
C: Ferritin
D: Ferritin
hetero molecules

E: Ferritin
C: Ferritin
D: Ferritin
hetero molecules

E: Ferritin
C: Ferritin
D: Ferritin
hetero molecules

E: Ferritin
C: Ferritin
D: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)478,153100
Polymers473,64124
Non-polymers4,51276
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_454x-1/2,y+1/2,z-1/21
crystal symmetry operation6_544-x+1/2,-y-1/2,z-1/21
crystal symmetry operation7_444-y-1/2,x-1/2,z-1/21
crystal symmetry operation8_554y+1/2,-x+1/2,z-1/21
Buried area91690 Å2
ΔGint-679 kcal/mol
Surface area138730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.374, 126.374, 177.109
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
11B-81-

GLN

21A-203-

ZN

31A-204-

ZN

41D-203-

ZN

51D-204-

ZN

61D-301-

HOH

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Components

#1: Protein
Ferritin


Mass: 19735.049 Da / Num. of mol.: 6 / Mutation: Q89R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penaeus japonicus (crustacean) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / 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
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.99 Å3/Da / Density % sol: 58.81 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / Details: 1.26 M (NH4)2SO4, 100 mM Tris (pH =8.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 42516 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.056 / Rrim(I) all: 0.147 / Χ2: 1.003 / Net I/σ(I): 4.5 / Num. measured all: 291156
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.6470.68821250.7850.2810.7430.54100
2.64-2.6970.61221220.8290.2510.6620.591100
2.69-2.7470.55921390.8230.2280.6040.525100
2.74-2.86.90.49721190.8640.2040.5380.552100
2.8-2.866.90.41621140.9020.1720.4510.59100
2.86-2.936.80.38221000.9160.1580.4140.623100
2.93-36.70.32321410.930.1340.350.661100
3-3.086.40.28821030.9450.1230.3140.696100
3.08-3.176.20.23521080.9570.1020.2570.838100
3.17-3.287.10.22621150.960.0910.2430.908100
3.28-3.397.10.20521570.9680.0830.2210.913100
3.39-3.5370.18820880.9760.0770.2031.09100
3.53-3.6970.20321380.9670.0840.221.618100
3.69-3.886.90.15621180.9810.0640.1691.319100
3.88-4.136.30.12421230.9870.0540.1351.548100
4.13-4.457.10.10421350.990.0420.1131.6100
4.45-4.897.20.09321310.9920.0370.11.543100
4.89-5.66.90.08721330.9940.0350.0941.258100
5.6-7.056.60.0821450.9940.0330.0871.1100
7.05-506.70.06421620.9960.0270.071.52199.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KH1

6kh1


Resolution: 2.602→34.107 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 28.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2721 2027 4.77 %
Rwork0.1936 40460 -
obs0.1973 42487 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.48 Å2 / Biso mean: 54.8772 Å2 / Biso min: 29.07 Å2
Refinement stepCycle: final / Resolution: 2.602→34.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8232 0 19 16 8267
Biso mean--57.51 62.12 -
Num. residues----1002
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.602-2.66670.31141380.2332291399
2.6667-2.73880.35921470.22992863100
2.7388-2.81930.29121500.22562844100
2.8193-2.91030.34941460.22012899100
2.9103-3.01430.3551430.2262873100
3.0143-3.13490.28761450.21932907100
3.1349-3.27740.33191470.21652855100
3.2774-3.45010.31941420.20842893100
3.4501-3.6660.33051420.21082898100
3.666-3.94870.24631330.19572913100
3.9487-4.34530.24611480.1712892100
4.3453-4.97240.22321620.15832880100
4.9724-6.25840.27461430.19512907100
6.2584-34.1070.21171410.171292399

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