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- PDB-3fi6: apo-H49AFr with high content of Pd ions -

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Basic information

Entry
Database: PDB / ID: 3fi6
Titleapo-H49AFr with high content of Pd ions
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / Iron storage / light chain apoferritin
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, 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
: / PALLADIUM ION / Ferritin light chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAbe, M. / Ueno, T. / Hirata, K. / Suzuki, M. / Abe, S. / Shimizu, N. / Yamaoto, M. / Takata, M. / Watanabe, Y.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Process of Accumulation of Metal Ions on the Interior Surface of apo-Ferritin: Crystal Structures of a Series of apo-Ferritins Containing Variable Quantities of Pd(II) Ions
Authors: Ueno, T. / Abe, M. / Hirata, K. / Abe, S. / Suzuki, M. / Shimizu, N. / Yamamoto, M. / Takata, M. / Watanabe, Y.
History
DepositionDec 11, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 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 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,84911
Polymers19,7891
Non-polymers1,06010
Water3,009167
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)500,380264
Polymers474,94424
Non-polymers25,436240
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 area91670 Å2
ΔGint-616.3 kcal/mol
Surface area138430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.701, 180.701, 180.701
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-209-

CD

21A-1142-

HOH

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Components

#1: Protein Ferritin light chain / Ferritin L subunit


Mass: 19789.314 Da / Num. of mol.: 1 / Mutation: H49A, L93P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: FTL / Plasmid: pMK2 / Production host: Escherichia coli (E. coli) / Strain (production host): Nova Blue / References: UniProt: P02791
#2: Chemical
ChemComp-PD / PALLADIUM ION


Mass: 106.420 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Pd
#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.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FEATURE OF UNIPROT (FRIL_HORSE, P02791) SHOWS CONFLICT AT THIS POSITION: L -> P (IN REF. 2).'

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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: 60.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Ammonium sulfate, Cadmium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 23, 2008
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 24004 / % possible obs: 100 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 57.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 8 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DAT

1dat


Resolution: 1.8→21.3 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.928 / SU B: 1.755 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22526 1228 5.1 %RANDOM
Rwork0.19566 ---
obs0.19712 22765 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.797 Å2
Refinement stepCycle: LAST / Resolution: 1.8→21.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1406 0 14 167 1587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221440
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.971951
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7065184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1723.68476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91715261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4421514
X-RAY DIFFRACTIONr_chiral_restr0.0940.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021106
X-RAY DIFFRACTIONr_nbd_refined0.230.2731
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2998
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2133
X-RAY DIFFRACTIONr_metal_ion_refined0.1680.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.216
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1210.21
X-RAY DIFFRACTIONr_mcbond_it0.9961.5900
X-RAY DIFFRACTIONr_mcangle_it1.46821387
X-RAY DIFFRACTIONr_scbond_it2.463603
X-RAY DIFFRACTIONr_scangle_it3.7424.5557
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 85 -
Rwork0.22 1623 -
obs--100 %

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