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- PDB-5e1u: Crystal structure of IrCp*-apo-Fr -

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Basic information

Entry
Database: PDB / ID: 5e1u
TitleCrystal structure of IrCp*-apo-Fr
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / IRON STORAGE
Function / homology
Function and homology information


ferritin complex / autolysosome / ferric iron binding / autophagosome / iron ion transport / ferrous iron binding / cytoplasmic vesicle / intracellular iron ion homeostasis / iron ion binding / 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
: / IRIDIUM (III) ION / Chem-RIR / Ferritin light chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsMaity, B. / Fukumori, K. / Abe, S. / Ueno, T.
CitationJournal: Chem.Commun.(Camb.) / Year: 2016
Title: Immobilization of two organometallic complexes into a single cage to construct protein-based microcompartments
Authors: Maity, B. / Fukumori, K. / Abe, S. / Ueno, T.
History
DepositionSep 30, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,65811
Polymers19,8721
Non-polymers1,78510
Water3,351186
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)519,785264
Polymers476,93824
Non-polymers42,847240
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 area101590 Å2
ΔGint-931 kcal/mol
Surface area139340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.035, 181.035, 181.035
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-207-

CD

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ferritin light chain / Ferritin L subunit


Mass: 19872.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: FTL / Production host: Escherichia coli (E. coli) / References: UniProt: P02791

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Non-polymers , 5 types, 196 molecules

#2: Chemical
ChemComp-IR3 / IRIDIUM (III) ION


Mass: 192.217 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ir
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-RIR / [(1,2,3,4,5-Eta)-1,2,3,4,5-Pentamethylcyclopentadienyl]iridium(III)


Mass: 327.443 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15Ir
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulphate, Cadmium Sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1.10461 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2014
RadiationMonochromator: Fixed exit Si (111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.10461 Å / Relative weight: 1
ReflectionResolution: 1.56→40 Å / Num. obs: 36642 / % possible obs: 99.9 % / Redundancy: 11 % / Net I/σ(I): 67.5
Reflection shellResolution: 1.56→1.59 Å / Redundancy: 11 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 10.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOLREPmodel building
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DAT

1dat


Resolution: 1.56→26.13 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 0.865 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18769 1829 5 %RANDOM
Rwork0.16788 ---
obs0.16889 34755 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.898 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.56→26.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1389 0 28 186 1603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0191473
X-RAY DIFFRACTIONr_bond_other_d0.0020.021416
X-RAY DIFFRACTIONr_angle_refined_deg3.0491.9922010
X-RAY DIFFRACTIONr_angle_other_deg1.04733244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5975182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88524.05179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66915270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7951513
X-RAY DIFFRACTIONr_chiral_restr0.1760.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021672
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02357
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_it2.2241.577701
X-RAY DIFFRACTIONr_mcbond_other2.1981.57700
X-RAY DIFFRACTIONr_mcangle_it3.0242.353877
X-RAY DIFFRACTIONr_mcangle_other3.0242.36878
X-RAY DIFFRACTIONr_scbond_it3.6381.953771
X-RAY DIFFRACTIONr_scbond_other3.6351.954772
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3372.811108
X-RAY DIFFRACTIONr_long_range_B_refined6.8614.4891889
X-RAY DIFFRACTIONr_long_range_B_other6.74913.6021776
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.56→1.601 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 140 -
Rwork0.162 2493 -
obs--100 %

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