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- PDB-7bom: Crystal structure of recombinant horse spleen apo-R52C/E56C/R59C/... -

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Basic information

Entry
Database: PDB / ID: 7bom
TitleCrystal structure of recombinant horse spleen apo-R52C/E56C/R59C/E63C-Fr immobilized with gold ions.
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
: / : / Ferritin light chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsHishikawa, Y. / Maity, B. / Ito, N. / Abe, S. / Lu, D. / Ueno, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Chem Lett. / Year: 2021
Title: Design of Multinuclear Gold Binding Site at the Two-fold Symmetric Interface of the Ferritin Cage
Authors: Hishikawa, Y. / Maity, B. / Ito, N. / Abe, S. / Lu, D. / Ueno, T.
History
DepositionMar 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
X: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,85522
Polymers19,7121
Non-polymers3,14221
Water2,378132
1
X: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)548,511528
Polymers473,09724
Non-polymers75,414504
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 area105280 Å2
ΔGint-859 kcal/mol
Surface area131380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.716, 181.716, 181.716
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
11X-213-

CD

21X-214-

CD

31X-215-

CD

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Components

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Protein , 1 types, 1 molecules X

#1: Protein Ferritin light chain / Ferritin L subunit


Mass: 19712.383 Da / Num. of mol.: 1 / Mutation: R53C,E57C,R60C,E64C
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, 153 molecules

#2: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Au / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 3.28 Å3/Da / Density % sol: 62.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulphate, Cadmium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1.03556 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03556 Å / Relative weight: 1
ReflectionResolution: 1.93→30.73 Å / Num. obs: 19871 / % possible obs: 99.85 % / Redundancy: 11.6 % / CC1/2: 0.98 / Rpim(I) all: 0.018 / Rrim(I) all: 0.061 / Net I/σ(I): 12.76
Reflection shellResolution: 1.93→2 Å / Num. unique obs: 1952 / CC1/2: 0.98 / CC star: 0.995 / Rpim(I) all: 0.094 / Rrim(I) all: 0.319 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DAT

1dat


Resolution: 1.93→30.73 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.196 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.11
RfactorNum. reflection% reflectionSelection details
Rfree0.19614 970 4.9 %RANDOM
Rwork0.16319 ---
obs0.16475 18901 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.678 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.93→30.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1334 0 28 132 1494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131412
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171296
X-RAY DIFFRACTIONr_angle_refined_deg1.7241.631913
X-RAY DIFFRACTIONr_angle_other_deg1.5451.5753004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2775184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66722.19582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37415247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4471511
X-RAY DIFFRACTIONr_chiral_restr0.0990.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021625
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02312
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_it2.2932.281703
X-RAY DIFFRACTIONr_mcbond_other2.242.27701
X-RAY DIFFRACTIONr_mcangle_it3.2413.4883
X-RAY DIFFRACTIONr_mcangle_other3.2283.398883
X-RAY DIFFRACTIONr_scbond_it3.72.646707
X-RAY DIFFRACTIONr_scbond_other3.6932.617701
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4583.781017
X-RAY DIFFRACTIONr_long_range_B_refined7.1928.321680
X-RAY DIFFRACTIONr_long_range_B_other7.00427.941654
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.931→1.981 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.187 60 -
Rwork0.179 1381 -
obs--100 %

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