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- PDB-3ka9: Frog M-ferritin, EEH mutant, with cobalt -

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Basic information

Entry
Database: PDB / ID: 3ka9
TitleFrog M-ferritin, EEH 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 / ferrous iron binding / intracellular iron ion homeostasis / 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: 1.45 Å
AuthorsTosha, T. / Ng, H.L. / Theil, E. / Alber, T. / Bhattasali, O.
CitationJournal: To be Published
Title: Frog M-ferritin, EEH mutant, with cobalt
Authors: Tosha, T. / Ng, H.L. / Theil, E. / Alber, T. / Bhattasali, O.
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)21,35918
Polymers20,6471
Non-polymers71117
Water5,332296
1
A: Ferritin, middle subunit
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)512,605432
Polymers495,53324
Non-polymers17,072408
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_665-y+1,-x+1,-z1
crystal symmetry operation15_565y,-x+1,z1
crystal symmetry operation16_655-y+1,x,z1
crystal symmetry operation33_554y,z+1/2,x-1/21
crystal symmetry operation34_655-y+1,z+1/2,-x+1/21
crystal symmetry operation35_555y,-z+1/2,-x+1/21
crystal symmetry operation36_654-y+1,-z+1/2,x-1/21
crystal symmetry operation41_555x,z+1/2,-y+1/21
crystal symmetry operation42_654-x+1,z+1/2,y-1/21
crystal symmetry operation43_655-x+1,-z+1/2,-y+1/21
crystal symmetry operation44_554x,-z+1/2,y-1/21
crystal symmetry operation53_554z+1/2,x,y-1/21
crystal symmetry operation54_565z+1/2,-x+1,-y+1/21
crystal symmetry operation55_564-z+1/2,-x+1,y-1/21
crystal symmetry operation56_555-z+1/2,x,-y+1/21
crystal symmetry operation69_555z+1/2,y,-x+1/21
crystal symmetry operation70_564z+1/2,-y+1,x-1/21
crystal symmetry operation71_554-z+1/2,y,x-1/21
crystal symmetry operation72_565-z+1/2,-y+1,-x+1/21
Buried area92630 Å2
ΔGint-253 kcal/mol
Surface area132810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.452, 183.452, 183.452
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-

CO

41A-185-

CL

51A-187-

CL

61A-188-

MG

71A-274-

HOH

81A-459-

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: 20647.225 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.: 7 / 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


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


Mass: 18.015 Da / Num. of mol.: 296 / 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: 3.11 Å3/Da / Density % sol: 60.51 %
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: 1.45→50 Å / Num. obs: 47219 / % possible obs: 100 % / Redundancy: 15.6 % / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 25.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.45-1.5315.10.798110251067730.798100
1.53-1.6215.50.5261.59905963940.526100
1.62-1.7315.80.3622.19562560430.362100
1.73-1.87160.2343.39035156490.234100
1.87-2.05160.1455.38362852140.145100
2.05-2.2915.90.0888.57597447650.088100
2.29-2.6515.80.0749.36647742180.074100
2.65-3.24150.04913.95408736110.049100
3.24-4.5915.70.03219.34451728420.03299.6
4.59-5014.80.0313.52528817100.03100

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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: 1.45→50 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.515 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.165 2387 5.1 %RANDOM
Rwork0.129 ---
obs0.131 47201 99.91 %-
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: 71.52 Å2 / Biso mean: 15.709 Å2 / Biso min: 3.29 Å2
Refinement stepCycle: LAST / Resolution: 1.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1429 0 17 296 1742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0211528
X-RAY DIFFRACTIONr_bond_other_d0.0040.021058
X-RAY DIFFRACTIONr_angle_refined_deg1.9491.9422069
X-RAY DIFFRACTIONr_angle_other_deg2.03532583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1365192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.60924.66790
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86315290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7361510
X-RAY DIFFRACTIONr_chiral_restr0.1530.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021731
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02318
X-RAY DIFFRACTIONr_mcbond_it2.1461.5890
X-RAY DIFFRACTIONr_mcbond_other0.9151.5359
X-RAY DIFFRACTIONr_mcangle_it2.93921437
X-RAY DIFFRACTIONr_scbond_it5.0073638
X-RAY DIFFRACTIONr_scangle_it6.8724.5622
X-RAY DIFFRACTIONr_rigid_bond_restr2.42232586
X-RAY DIFFRACTIONr_sphericity_free13.3423313
X-RAY DIFFRACTIONr_sphericity_bonded4.1832545
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 172 -
Rwork0.283 3238 -
all-3410 -
obs--99.42 %

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