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- PDB-6jps: Human H chain ferritin mutant-MBP -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6jps
TitleHuman H chain ferritin mutant-MBP
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / ferritin / mercuric ion binding peptide
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 / Ferritin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.503 Å
AuthorsWang, Y. / Zang, J. / Chen, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)2018YFD0901004 China
CitationJournal: Analyst / Year: 2019
Title: Re-designing ferritin nanocages for mercuric ion detection.
Authors: Wang, Y. / Chen, H. / Zang, J. / Zhang, X. / Zhao, G.
History
DepositionMar 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 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
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin
I: Ferritin
J: Ferritin
K: Ferritin
L: Ferritin
M: Ferritin
N: Ferritin
O: Ferritin
P: Ferritin
Q: Ferritin
R: Ferritin
S: Ferritin
T: Ferritin
U: Ferritin
V: Ferritin
W: Ferritin
X: Ferritin


Theoretical massNumber of molelcules
Total (without water)522,26924
Polymers522,26924
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area95220 Å2
ΔGint-213 kcal/mol
Surface area140820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)217.524, 217.524, 146.821
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42

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Components

#1: Protein ...
Ferritin


Mass: 21761.203 Da / Num. of mol.: 24 / Mutation: K86Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NS36, UniProt: P02794*PLUS

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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: 3.33 Å3/Da / Density % sol: 63.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: magnesium chloride, Tris, 1,6-hexanediol

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3.503→47.75 Å / Num. obs: 85322 / % possible obs: 98 % / Redundancy: 1 % / CC1/2: 0.945 / Net I/σ(I): 1.5
Reflection shellResolution: 3.503→3.628 Å / CC1/2: 0.945

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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: 1fha

1fha


Resolution: 3.503→47.75 Å / SU ML: 0.69 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 48.22
RfactorNum. reflection% reflection
Rfree0.3987 1997 2.36 %
Rwork0.3393 --
obs0.3409 85322 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.503→47.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33912 0 0 0 33912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00334608
X-RAY DIFFRACTIONf_angle_d0.48246632
X-RAY DIFFRACTIONf_dihedral_angle_d21.34320904
X-RAY DIFFRACTIONf_chiral_restr0.0354896
X-RAY DIFFRACTIONf_plane_restr0.0036168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5029-3.59050.48311400.37285880X-RAY DIFFRACTION99
3.5905-3.68750.45851440.36735975X-RAY DIFFRACTION99
3.6875-3.7960.43831440.36555917X-RAY DIFFRACTION99
3.796-3.91850.43711410.37755882X-RAY DIFFRACTION99
3.9185-4.05850.48831430.37415902X-RAY DIFFRACTION99
4.0585-4.22090.4181380.35915866X-RAY DIFFRACTION98
4.2209-4.41290.40551430.34665922X-RAY DIFFRACTION99
4.4129-4.64540.35631460.32935925X-RAY DIFFRACTION99
4.6454-4.93620.40571420.34085930X-RAY DIFFRACTION99
4.9362-5.31690.37241430.32855882X-RAY DIFFRACTION98
5.3169-5.85120.42711450.3315943X-RAY DIFFRACTION99
5.8512-6.69610.331390.32785978X-RAY DIFFRACTION99
6.6961-8.42970.34891420.29415925X-RAY DIFFRACTION98
8.4297-49.65420.31911470.28575730X-RAY DIFFRACTION93

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