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- PDB-3ka8: Frog M-ferritin, EQH mutant, with cobalt -

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Basic information

Entry
Database: PDB / ID: 3ka8
TitleFrog M-ferritin, EQH mutant, with cobalt
ComponentsFerritin, middle subunit
KeywordsOXIDOREDUCTASE / IRON STORAGE / DIIRON / Iron / Metal-binding
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / 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, middle subunit
Similarity search - Component
Biological speciesRana catesbeiana (American bullfrog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 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 19, 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 / 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)21,33519
Polymers20,6461
Non-polymers68918
Water5,657314
1
A: Ferritin, middle subunit
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)512,038456
Polymers495,51024
Non-polymers16,528432
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Buried area93530 Å2
ΔGint-300 kcal/mol
Surface area130400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.490, 183.490, 183.490
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-181-

MG

41A-182-

MG

51A-184-

CL

61A-342-

HOH

71A-456-

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: 20646.240 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.: 5 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 3.12 Å3/Da / Density % sol: 60.54 %
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: 1.35→50 Å / Num. obs: 58309 / % possible obs: 100 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 19.2
Reflection shell

% possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value
1.35-1.429.40.8350.97894283720.835
1.42-1.5113.60.5441.410762879080.544
1.51-1.6113.80.342.210300474720.34
1.61-1.7413.90.2273.39663369570.227
1.74-1.9113.90.1445.38961764570.144
1.91-2.1313.90.0878.58120958620.087
2.13-2.4613.70.0758.97149352020.075
2.46-3.0213.40.06110.45964744640.061
3.02-4.2713.20.03714.14650835150.037
4.27-50130.03113.42727721000.031

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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: 1.35→50 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / Occupancy max: 1 / Occupancy min: 0.16 / SU B: 1.13 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.153 2951 5.1 %RANDOM
Rwork0.13 ---
obs0.131 58294 99.97 %-
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: 58.4 Å2 / Biso mean: 14.365 Å2 / Biso min: 6.72 Å2
Refinement stepCycle: LAST / Resolution: 1.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1416 0 18 314 1748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0211544
X-RAY DIFFRACTIONr_bond_other_d0.0020.021075
X-RAY DIFFRACTIONr_angle_refined_deg1.9571.9482096
X-RAY DIFFRACTIONr_angle_other_deg1.78532628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0795198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.96724.55690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30115297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5271511
X-RAY DIFFRACTIONr_chiral_restr0.1420.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021758
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02324
X-RAY DIFFRACTIONr_mcbond_it1.9371.5900
X-RAY DIFFRACTIONr_mcbond_other0.8111.5362
X-RAY DIFFRACTIONr_mcangle_it2.65721457
X-RAY DIFFRACTIONr_scbond_it4.6063644
X-RAY DIFFRACTIONr_scangle_it6.3734.5626
X-RAY DIFFRACTIONr_rigid_bond_restr2.12532619
X-RAY DIFFRACTIONr_sphericity_free13.3433332
X-RAY DIFFRACTIONr_sphericity_bonded3.95532575
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 200 -
Rwork0.378 4001 -
all-4201 -
obs--99.64 %

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