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- PDB-7eml: Structure of IrCp* immobilized apo-D38H-rHLFr -

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Basic information

Entry
Database: PDB / ID: 7eml
TitleStructure of IrCp* immobilized apo-D38H-rHLFr
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / Iron storage protein / Ir binding
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
: / : / Chem-RIR / Ferritin light chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsTaher, M. / Maity, B. / Nakane, T. / Abe, S. / Ueno, T. / Mazumdar, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Controlled Uptake of an Iridium Complex inside Engineered apo-Ferritin Nanocages: Study of Structure and Catalysis.
Authors: Taher, M. / Maity, B. / Nakane, T. / Abe, S. / Ueno, T. / Mazumdar, S.
History
DepositionApr 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,90616
Polymers19,8951
Non-polymers2,01015
Water4,288238
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)525,734384
Polymers477,49224
Non-polymers48,242360
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 area100840 Å2
ΔGint-1111 kcal/mol
Surface area138150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.937, 181.937, 181.937
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-206-

CD

21A-207-

CD

31A-208-

CD

41A-210-

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: 19895.486 Da / Num. of mol.: 1 / Mutation: D38H
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 , 7 types, 253 molecules

#2: 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-IR / IRIDIUM ION


Mass: 192.217 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ir / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.19 Å3/Da / Density % sol: 61.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Ammonium sulfate (0.5-1.0M), Cadmium sulfate(12-20mM)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.05 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.25→45.526 Å / Num. obs: 71305 / % possible obs: 100 % / Redundancy: 72.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.2 / Net I/σ(I): 23.1
Reflection shellResolution: 1.25→1.27 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 71305 / CC1/2: 0.82

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DAT

1dat


Resolution: 1.25→41.739 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.177 / WRfactor Rwork: 0.167 / SU B: 0.482 / SU ML: 0.021 / Average fsc free: 0.9589 / Average fsc work: 0.9613 / Cross valid method: FREE R-VALUE / ESU R: 0.037 / ESU R Free: 0.038
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1828 3571 5.008 %
Rwork0.1714 67732 -
all0.172 --
obs-71303 99.989 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 14.399 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.25→41.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1381 0 39 238 1658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0131573
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171486
X-RAY DIFFRACTIONr_angle_refined_deg2.2011.6622162
X-RAY DIFFRACTIONr_angle_other_deg1.5811.593463
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6545210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33922.26897
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.42715296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.421513
X-RAY DIFFRACTIONr_chiral_restr0.1240.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021775
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02340
X-RAY DIFFRACTIONr_nbd_refined0.2930.2403
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.21308
X-RAY DIFFRACTIONr_nbtor_refined0.1930.2727
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0970.2643
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2490.2144
X-RAY DIFFRACTIONr_metal_ion_refined0.3120.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.330.221
X-RAY DIFFRACTIONr_nbd_other0.2050.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.170.235
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.410.22
X-RAY DIFFRACTIONr_mcbond_it1.491.242731
X-RAY DIFFRACTIONr_mcbond_other1.4821.237730
X-RAY DIFFRACTIONr_mcangle_it2.2931.861921
X-RAY DIFFRACTIONr_mcangle_other2.2921.866922
X-RAY DIFFRACTIONr_scbond_it2.6951.557842
X-RAY DIFFRACTIONr_scbond_other2.6111.548835
X-RAY DIFFRACTIONr_scangle_it3.982.2311201
X-RAY DIFFRACTIONr_scangle_other3.9642.211190
X-RAY DIFFRACTIONr_lrange_it5.9817.0611926
X-RAY DIFFRACTIONr_lrange_other5.70416.1161859
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.25-1.2820.3762660.39348980.39251640.9190.9151000.363
1.282-1.3180.3542480.30547940.30850430.9260.9399.98020.275
1.318-1.3560.2522540.24546780.24549320.9460.9451000.217
1.356-1.3970.2142370.20845390.20847760.9480.9541000.178
1.397-1.4430.1982360.18544010.18646370.9540.9551000.159
1.443-1.4940.182330.15642740.15745070.9590.9671000.137
1.494-1.550.1672200.14641240.14743440.9670.9721000.131
1.55-1.6130.162250.14539450.14641700.9720.9731000.133
1.613-1.6850.1531840.13938470.1440310.9730.9761000.129
1.685-1.7670.1582030.14336520.14438550.970.9751000.135
1.767-1.8620.161730.14634990.14736720.9740.9761000.14
1.862-1.9750.1721790.15733050.15834840.9720.9741000.154
1.975-2.1110.1731530.16231550.16233080.9720.9761000.161
2.111-2.280.1461630.14629060.14630690.980.981000.148
2.28-2.4970.1611520.1426900.14128420.9750.9771000.147
2.497-2.790.1651210.14624820.14726030.9720.9741000.155
2.79-3.2190.1651160.15421990.15423150.970.9691000.168
3.219-3.9370.177960.15918860.1619820.9680.9711000.178
3.937-5.5430.191750.19515100.19515860.9720.97499.9370.219
5.543-41.7390.345370.3199480.329850.9280.9391000.347

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