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- PDB-3ka6: Frog M-ferritin, EED mutant, with cobalt -

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Basic information

Entry
Database: PDB / ID: 3ka6
TitleFrog M-ferritin, EED mutant, with cobalt
ComponentsFerritin, middle subunit
KeywordsOXIDOREDUCTASE / IRON STORAGE / DIIRON / Iron / Metal-binding
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
: / Ferritin, middle subunit
Similarity search - Component
Biological speciesRana catesbeiana (American bullfrog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsTosha, T. / Ng, H.L. / Theil, E. / Alber, T. / Bhattasali, O.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Moving Metal Ions through Ferritin-Protein Nanocages from Three-Fold Pores to Catalytic Sites.
Authors: Tosha, T. / Ng, H.L. / Bhattasali, O. / Alber, T. / Theil, E.C.
History
DepositionOct 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferritin, middle subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,47720
Polymers20,6241
Non-polymers85319
Water5,801322
1
A: Ferritin, middle subunit
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)515,444480
Polymers494,98024
Non-polymers20,464456
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation17_556x,z,-y+11
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_566-x,-z+1,-y+11
crystal symmetry operation20_565x,-z+1,y1
crystal symmetry operation57_455y-1/2,z,x+1/21
crystal symmetry operation58_555-y+1/2,z,-x+1/21
crystal symmetry operation59_465y-1/2,-z+1,-x+1/21
crystal symmetry operation60_565-y+1/2,-z+1,x+1/21
crystal symmetry operation69_455z-1/2,y,-x+1/21
crystal symmetry operation70_465z-1/2,-y+1,x+1/21
crystal symmetry operation71_555-z+1/2,y,x+1/21
crystal symmetry operation72_565-z+1/2,-y+1,-x+1/21
crystal symmetry operation77_455z-1/2,x+1/2,y1
crystal symmetry operation78_456z-1/2,-x+1/2,-y+11
crystal symmetry operation79_555-z+1/2,-x+1/2,y1
crystal symmetry operation80_556-z+1/2,x+1/2,-y+11
crystal symmetry operation85_456y-1/2,x+1/2,-z+11
crystal symmetry operation86_556-y+1/2,-x+1/2,-z+11
crystal symmetry operation87_455y-1/2,-x+1/2,z1
crystal symmetry operation88_555-y+1/2,x+1/2,z1
Buried area103240 Å2
ΔGint-890 kcal/mol
Surface area133450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.708, 183.708, 183.708
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-176-

CO

21A-180-

CO

31A-185-

CO

41A-186-

MG

51A-189-

CL

61A-430-

HOH

71A-488-

HOH

DetailsBiological unit is a 24-mer generated by F432 symmetry

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Components

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


Mass: 20624.166 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rana catesbeiana (American bullfrog) / Production host: Escherichia coli (E. coli) / References: UniProt: P07798, ferroxidase
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 3.13 Å3/Da / Density % sol: 60.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 2M MgCl2, 0.1M Bicine pH 9.0, 0.1M CoCl2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
Details: Mirror 1: plane parabola Pt and Rh-coated Invar steel. Mirror 2: torroid Pt and Rh-coated Si
RadiationMonochromator: KOHZU: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 52583 / % possible obs: 100 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 28.8
Reflection shell

% possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value
1.4-1.489.20.880.96912375350.88
1.48-1.5713.50.5171.59623271510.517
1.57-1.6713.70.3322.39166667070.332
1.67-1.8113.80.2173.58645062800.217
1.81-1.9813.70.1295.97999858260.129
1.98-2.2113.70.074107222452880.074
2.21-2.5613.40.06111.56301147010.061
2.56-3.1312.80.0513.15123240150.05
3.13-4.4312.60.03217.94004331790.032
4.43-5012.60.02618.52398619010.026

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.2.5data scaling
PHASERphasing
REFMAC5.4.0077refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3KA3

3ka3


Resolution: 1.4→50 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / Occupancy max: 1 / Occupancy min: 0.16 / SU B: 1.344 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.166 2678 5.1 %RANDOM
Rwork0.139 ---
obs0.141 52574 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 74.57 Å2 / Biso mean: 16.499 Å2 / Biso min: 4.86 Å2
Refinement stepCycle: LAST / Resolution: 1.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1415 0 19 322 1756
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0211543
X-RAY DIFFRACTIONr_bond_other_d0.0020.021061
X-RAY DIFFRACTIONr_angle_refined_deg2.1021.9422098
X-RAY DIFFRACTIONr_angle_other_deg2.02432596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5425199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.84424.67492
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00115290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3361510
X-RAY DIFFRACTIONr_chiral_restr0.1280.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021762
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02323
X-RAY DIFFRACTIONr_mcbond_it1.9951.5897
X-RAY DIFFRACTIONr_mcbond_other0.8031.5361
X-RAY DIFFRACTIONr_mcangle_it2.8621453
X-RAY DIFFRACTIONr_scbond_it4.7073646
X-RAY DIFFRACTIONr_scangle_it6.5594.5631
X-RAY DIFFRACTIONr_rigid_bond_restr2.25932604
X-RAY DIFFRACTIONr_sphericity_free12.6923341
X-RAY DIFFRACTIONr_sphericity_bonded3.9332558
LS refinement shellResolution: 1.4→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.449 197 -
Rwork0.411 3646 -
all-3843 -
obs--99.97 %

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