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- PDB-3wnw: Structure of Mouse H-chain modified ferritin -

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Basic information

Entry
Database: PDB / ID: 3wnw
TitleStructure of Mouse H-chain modified ferritin
ComponentsFerritin heavy chain
KeywordsOXIDOREDUCTASE / Ferritin / Four Helix Boundle / Iron Storage / blood / cells
Function / homology
Function and homology information


Iron uptake and transport / Golgi Associated Vesicle Biogenesis / iron ion sequestering activity / negative regulation of ferroptosis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / endocytic vesicle lumen / Neutrophil degranulation ...Iron uptake and transport / Golgi Associated Vesicle Biogenesis / iron ion sequestering activity / negative regulation of ferroptosis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / endocytic vesicle lumen / Neutrophil degranulation / ferric iron binding / autophagosome / ferrous iron binding / iron ion transport / intracellular iron ion homeostasis / immune response / iron ion binding / negative regulation of cell population proliferation / mitochondrion / extracellular region / identical protein binding / membrane / cytosol
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin, core subunit, four-helix bundle / 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 / Ferritin, core subunit, four-helix bundle / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsZarivach, R. / Lewin, L.
CitationJournal: To be Published
Title: Studies of ferritin-M6A
Authors: Zarivach, R. / Lewin, L.
History
DepositionDec 17, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
E: Ferritin heavy chain
F: Ferritin heavy chain
G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,70350
Polymers289,81012
Non-polymers1,89338
Water24,7531374
1
A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)583,406100
Polymers579,62024
Non-polymers3,78676
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area103340 Å2
ΔGint-636 kcal/mol
Surface area143050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.145, 218.145, 147.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11B-202-

FE

21H-202-

FE

31L-302-

HOH

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Ferritin heavy chain / Ferritin H subunit / Ferritin heavy chain / N-terminally processed


Mass: 24150.836 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fth1, Fth / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: UniProt: P09528, ferroxidase

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Non-polymers , 5 types, 1412 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1374 / 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: 3.03 Å3/Da / Density % sol: 59.42 % / Mosaicity: 0.787 °
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Na-cacodylate PH 6.5, 0.2 M Mg-Ac, 30% MPD, vapor diffusion, sitting drop, temperature 286K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.947 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.947 Å / Relative weight: 1
ReflectionResolution: 2.24→50 Å / Num. all: 169360 / Num. obs: 161908 / % possible obs: 95.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Rmerge(I) obs: 0.143 / Χ2: 1.949 / Net I/σ(I): 5.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.25-2.293.70.56180081.546195.5
2.29-2.333.70.56179521.51195.1
2.33-2.383.70.46179361.537194.8
2.38-2.423.80.44879301.552194.7
2.42-2.483.80.41979131.511194.2
2.48-2.533.90.39178211.553193.6
2.53-2.640.37878121.669192.8
2.6-2.6740.31677331.649192.2
2.67-2.7540.27476941.645191.3
2.75-2.834.10.24675631.718190
2.83-2.9440.20776201.718190.6
2.94-3.0540.18178651.824193.5
3.05-3.193.90.15681371.844196.2
3.19-3.3640.1482991.979198
3.36-3.574.30.12184322.237199.4
3.57-3.855.30.1184782.489199.9
3.85-4.236.60.09885322.565199.9
4.23-4.857.30.08685412.564199.8
4.85-6.17.60.08586392.054199.8
6.1-508.10.05490031.85199.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.14data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IES

1ies


Resolution: 2.24→49.86 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.228 / WRfactor Rwork: 0.1866 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.6766 / SU B: 5.363 / SU ML: 0.133 / SU R Cruickshank DPI: 0.2511 / SU Rfree: 0.2158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.251 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2653 8052 5 %RANDOM
Rwork0.2204 ---
obs0.2227 160208 94.52 %-
all-169496 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.04 Å2 / Biso mean: 15.6891 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0 Å2-0 Å2
2---0.14 Å2-0 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.24→49.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17020 0 98 1374 18492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01917611
X-RAY DIFFRACTIONr_bond_other_d0.0010.0216490
X-RAY DIFFRACTIONr_angle_refined_deg1.9111.95223707
X-RAY DIFFRACTIONr_angle_other_deg0.924338026
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85552114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.4224.832983
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.835153252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.45815102
X-RAY DIFFRACTIONr_chiral_restr0.1040.22476
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0220156
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024238
X-RAY DIFFRACTIONr_mcbond_it1.3121.3618363
X-RAY DIFFRACTIONr_mcbond_other1.3121.3618362
X-RAY DIFFRACTIONr_mcangle_it2.1472.02910448
LS refinement shellResolution: 2.242→2.3 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 572 -
Rwork0.278 11041 -
all-11613 -
obs--93.45 %

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