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- PDB-4p18: Crystal Structure of frog M ferritin mutant D80K -

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Basic information

Entry
Database: PDB / ID: 4p18
TitleCrystal Structure of frog M ferritin mutant D80K
ComponentsFerritin, middle subunit
KeywordsOXIDOREDUCTASE / ferroxidase / point mutation / intersubunit electrostatic interactions / frog-M ferritin mutant D80K
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis
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
ACETATE ION / Ferritin, middle subunit
Similarity search - Component
Biological speciesRana catesbeiana (American bullfrog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsPozzi, C. / Di Pisa, F. / Mangani, S. / Bernacchioni, C. / Ghini, V. / Turano, P.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Loop electrostatics modulates the intersubunit interactions in ferritin.
Authors: Bernacchioni, C. / Ghini, V. / Pozzi, C. / Di Pisa, F. / Theil, E.C. / Turano, P.
History
DepositionFeb 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Nov 1, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Data collection / Derived calculations / Other / Source and taxonomy
Category: diffrn_source / entity_src_gen ...diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferritin, middle subunit
B: Ferritin, middle subunit
C: Ferritin, middle subunit
D: Ferritin, middle subunit
M: Ferritin, middle subunit
N: Ferritin, middle subunit
O: Ferritin, middle subunit
P: Ferritin, middle subunit
S: Ferritin, middle subunit
T: Ferritin, middle subunit
E: Ferritin, middle subunit
F: Ferritin, middle subunit
G: Ferritin, middle subunit
H: Ferritin, middle subunit
I: Ferritin, middle subunit
J: Ferritin, middle subunit
K: Ferritin, middle subunit
L: Ferritin, middle subunit
Q: Ferritin, middle subunit
R: Ferritin, middle subunit
U: Ferritin, middle subunit
V: Ferritin, middle subunit
W: Ferritin, middle subunit
X: Ferritin, middle subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)502,079133
Polymers495,29524
Non-polymers6,784109
Water91,0485054
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)238.930, 238.430, 119.690
Angle α, β, γ (deg.)90.00, 94.33, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-201-

CL

21B-306-

HOH

31B-307-

HOH

41E-307-

HOH

51J-314-

HOH

Detailsgel filtration

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Components

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Protein , 1 types, 24 molecules ABCDMNOPSTEFGHIJKLQRUVWX

#1: Protein ...
Ferritin, middle subunit / / Ferritin M / Ferritin H' / Ferritin X


Mass: 20637.273 Da / Num. of mol.: 24 / Mutation: D80K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rana catesbeiana (American bullfrog) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P07798, ferroxidase

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Non-polymers , 5 types, 5163 molecules

#2: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 51 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical...
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5054 / 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: 3.58 Å3/Da / Density % sol: 65.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1.0 M Ammonium sulfate, 0.1 M Sodium acetate pH 4.6
PH range: 4-5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→75.38 Å / Num. obs: 508671 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 9.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 5.3 / % possible all: 91.9

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Processing

SoftwareName: REFMAC / Version: 5.7.0032 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LQH

4lqh


Resolution: 1.91→75.35 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.887 / SU B: 2.69 / SU ML: 0.081 / Cross valid method: FREE R-VALUE / ESU R: 0.138 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23082 25123 5 %RANDOM
Rwork0.19618 ---
obs0.19791 474862 96.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.927 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.91→75.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33969 0 368 5054 39391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01935861
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.95248340
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.77354368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30724.7342015
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.706156687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.32915219
X-RAY DIFFRACTIONr_chiral_restr0.0840.25071
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0227565
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.450.6516841
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.7860.96921099
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.6520.76619018
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.2826.76363737
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.906→1.955 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 1740 -
Rwork0.25 31752 -
obs--87.76 %

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