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- PDB-6j7g: Human H-ferritin mutant-C90A/C102A/C130A/D144C -

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Basic information

Entry
Database: PDB / ID: 6j7g
TitleHuman H-ferritin mutant-C90A/C102A/C130A/D144C
ComponentsFerritin heavy chain
KeywordsOXIDOREDUCTASE / Human ferritin / Disulfide bond
Function / homology
Function and homology information


iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation ...iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation / autophagosome / ferric iron binding / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / iron ion transport / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / 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 iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / 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
Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.868 Å
AuthorsZang, J. / Chen, H. / Zhang, X. / Zhao, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China13730069 China
CitationJournal: Nat Commun / Year: 2019
Title: Disulfide-mediated conversion of 8-mer bowl-like protein architecture into three different nanocages.
Authors: Zang, J. / Chen, H. / Zhang, X. / Zhang, C. / Guo, J. / Du, M. / Zhao, G.
History
DepositionJan 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
M: Ferritin heavy chain
N: Ferritin heavy chain
O: Ferritin heavy chain
P: Ferritin heavy chain
Q: Ferritin heavy chain
R: Ferritin heavy chain
S: Ferritin heavy chain
T: Ferritin heavy chain
W: Ferritin heavy chain
X: Ferritin heavy chain
Y: Ferritin heavy chain
Z: Ferritin heavy chain
a: Ferritin heavy chain
b: Ferritin heavy chain
e: Ferritin heavy chain
f: Ferritin heavy chain


Theoretical massNumber of molelcules
Total (without water)488,26924
Polymers488,26924
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area89470 Å2
ΔGint-300 kcal/mol
Surface area141380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.380, 165.364, 164.865
Angle α, β, γ (deg.)90.00, 94.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ...
Ferritin heavy chain / Ferritin H subunit


Mass: 20344.531 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6 / Production host: Escherichia coli (E. coli) / References: UniProt: P02794, ferroxidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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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: 3.27 Å3/Da / Density % sol: 62.37 %
Crystal growTemperature: 293 K / Method: evaporation / Details: Amonium Sulfate, HEPES

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9979 Å / Relative weight: 1
ReflectionResolution: 3.86→40.87 Å / Num. obs: 54320 / % possible obs: 92 % / Redundancy: 2.3 % / CC1/2: 0.921 / Net I/σ(I): 2.7
Reflection shellResolution: 3.86→4.9 Å / CC1/2: 0.921

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FHA

2fha


Resolution: 3.868→40.87 Å / SU ML: 0.53 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 36.01
RfactorNum. reflection% reflection
Rfree0.3279 2730 5.03 %
Rwork0.2433 --
obs0.2477 54284 92.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.868→40.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32516 0 0 8 32524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01433200
X-RAY DIFFRACTIONf_angle_d1.53244737
X-RAY DIFFRACTIONf_dihedral_angle_d17.0519959
X-RAY DIFFRACTIONf_chiral_restr0.074680
X-RAY DIFFRACTIONf_plane_restr0.0075909
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8682-3.93850.3921000.24951943X-RAY DIFFRACTION66
3.9385-4.01420.34931590.24872735X-RAY DIFFRACTION94
4.0142-4.09610.37181350.25982710X-RAY DIFFRACTION93
4.0961-4.18510.32051180.242537X-RAY DIFFRACTION86
4.1851-4.28240.34871370.24832528X-RAY DIFFRACTION87
4.2824-4.38950.37641460.23142724X-RAY DIFFRACTION93
4.3895-4.50810.31031480.24222764X-RAY DIFFRACTION94
4.5081-4.64060.31251550.21822682X-RAY DIFFRACTION93
4.6406-4.79030.27931440.23932776X-RAY DIFFRACTION95
4.7903-4.96140.31511160.23972845X-RAY DIFFRACTION96
4.9614-5.15980.32021380.23962792X-RAY DIFFRACTION95
5.1598-5.39440.32571270.25192881X-RAY DIFFRACTION97
5.3944-5.67840.37221760.27432885X-RAY DIFFRACTION99
5.6784-6.03360.38911710.28182845X-RAY DIFFRACTION99
6.0336-6.49860.36021260.27582922X-RAY DIFFRACTION97
6.4986-7.15080.35241850.25952815X-RAY DIFFRACTION97
7.1508-8.18170.3571440.24592627X-RAY DIFFRACTION89
8.1817-10.29310.25481870.20932664X-RAY DIFFRACTION91
10.2931-49.87590.26931180.22332879X-RAY DIFFRACTION95

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