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- PDB-7emm: Crystal structure of IrCp* immobilized apo-R52H-rHLFr -

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Basic information

Entry
Database: PDB / ID: 7emm
TitleCrystal structure of IrCp* immobilized apo-R52H-rHLFr
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / Iron storage protein / Ir binding
Function / homology
Function and homology information


ferritin complex / autolysosome / intracellular sequestering of iron ion / autophagosome / ferric iron binding / ferrous iron binding / iron ion transport / cytoplasmic vesicle / iron ion binding / cytoplasm
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / : / 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

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Assembly

Deposited unit
A: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,97117
Polymers19,8531
Non-polymers2,11716
Water4,360242
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)527,299408
Polymers476,48124
Non-polymers50,818384
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
crystal symmetry operation13_554y,x,-z-11
crystal symmetry operation14_554-y,-x,-z-11
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation33_554y,z+1/2,x-1/21
crystal symmetry operation34_554-y,z+1/2,-x-1/21
crystal symmetry operation35_544y,-z-1/2,-x-1/21
crystal symmetry operation36_544-y,-z-1/2,x-1/21
crystal symmetry operation41_554x,z+1/2,-y-1/21
crystal symmetry operation42_554-x,z+1/2,y-1/21
crystal symmetry operation43_544-x,-z-1/2,-y-1/21
crystal symmetry operation44_544x,-z-1/2,y-1/21
crystal symmetry operation53_554z+1/2,x,y-1/21
crystal symmetry operation54_554z+1/2,-x,-y-1/21
crystal symmetry operation55_454-z-1/2,-x,y-1/21
crystal symmetry operation56_454-z-1/2,x,-y-1/21
crystal symmetry operation69_554z+1/2,y,-x-1/21
crystal symmetry operation70_554z+1/2,-y,x-1/21
crystal symmetry operation71_454-z-1/2,y,x-1/21
crystal symmetry operation72_454-z-1/2,-y,-x-1/21
Buried area95170 Å2
ΔGint-905 kcal/mol
Surface area138690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.064, 182.064, 182.064
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-204-

CD

21A-205-

CD

31A-206-

CD

41A-207-

CD

51A-524-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ferritin light chain / Ferritin L subunit


Mass: 19853.381 Da / Num. of mol.: 1 / Mutation: R52H
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 , 6 types, 258 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


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


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


Mass: 192.217 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ir / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 3.25 Å3/Da / Density % sol: 62.19 %
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→45.557 Å / Num. obs: 71449 / % possible obs: 100 % / Redundancy: 73.1 % / CC1/2: 1 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.02 / Rrim(I) all: 0.168 / Net I/σ(I): 2.5
Reflection shellResolution: 1.25→1.27 Å / Num. unique obs: 3467 / CC1/2: 0.848

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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→41.768 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.177 / WRfactor Rwork: 0.166 / SU B: 0.464 / SU ML: 0.02 / Average fsc free: 0.9589 / Average fsc work: 0.9634 / Cross valid method: FREE R-VALUE / ESU R: 0.038 / ESU R Free: 0.038
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1855 3614 5.059 %
Rwork0.1746 67828 -
all0.175 --
obs-71442 99.985 %
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: 13.196 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.25→41.768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1380 0 27 242 1649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0131546
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171450
X-RAY DIFFRACTIONr_angle_refined_deg2.1931.6332111
X-RAY DIFFRACTIONr_angle_other_deg1.5921.5773385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6885210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67322.18896
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.38315292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1071513
X-RAY DIFFRACTIONr_chiral_restr0.1180.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021771
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02340
X-RAY DIFFRACTIONr_nbd_refined0.2950.2379
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.21272
X-RAY DIFFRACTIONr_nbtor_refined0.190.2731
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0950.2638
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2640.2157
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0190.22
X-RAY DIFFRACTIONr_metal_ion_refined0.3070.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3810.215
X-RAY DIFFRACTIONr_nbd_other0.1680.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1540.236
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.4180.22
X-RAY DIFFRACTIONr_mcbond_it1.5341.142731
X-RAY DIFFRACTIONr_mcbond_other1.511.137730
X-RAY DIFFRACTIONr_mcangle_it2.3961.709921
X-RAY DIFFRACTIONr_mcangle_other2.3961.715922
X-RAY DIFFRACTIONr_scbond_it2.6611.405815
X-RAY DIFFRACTIONr_scbond_other2.6061.396808
X-RAY DIFFRACTIONr_scangle_it3.8872.0111169
X-RAY DIFFRACTIONr_scangle_other3.8831.9921158
X-RAY DIFFRACTIONr_lrange_it5.78415.7511916
X-RAY DIFFRACTIONr_lrange_other5.49914.521834
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
1.25-1.2830.4022540.40949320.40951860.9280.9241000.378
1.283-1.3180.3522640.32947810.3350470.9310.93799.96040.298
1.318-1.3560.32490.26946970.2749460.9270.9451000.239
1.356-1.3970.2322370.22445440.22447820.9540.95599.97910.193
1.397-1.4430.2222540.18443890.18646430.9490.9591000.158
1.443-1.4940.1622370.15542770.15645150.9680.96899.97790.135
1.494-1.550.172510.14641070.14843580.9670.9711000.131
1.55-1.6130.1662060.14739710.14841770.9680.9741000.134
1.613-1.6850.141890.14638540.14540430.9790.9781000.136
1.685-1.7670.1821960.15136570.15238530.9670.9761000.141
1.767-1.8630.1581850.15334990.15436840.9760.9771000.146
1.863-1.9750.1761670.16233320.16235000.9720.97599.97140.156
1.975-2.1110.1781700.16931220.16932920.970.9751000.165
2.111-2.280.1751700.15329050.15530750.9720.9771000.152
2.28-2.4970.1651350.13927190.14128540.970.9771000.143
2.497-2.790.1631250.14224940.14326190.9670.9751000.146
2.79-3.220.1551070.14722030.14723100.9750.9751000.154
3.22-3.9370.1341010.15618850.15419860.980.9761000.169
3.937-5.5440.224670.20715250.20815920.9770.9781000.22
5.544-41.7680.297500.3159350.3149850.9290.9351000.321

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