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- PDB-2zg9: Crystal Structure of Pd(allyl)/apo-H114AFr -

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Basic information

Entry
Database: PDB / ID: 2zg9
TitleCrystal Structure of Pd(allyl)/apo-H114AFr
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / IRON STORAGE PROTEIN / LIGHT CHAIN APOFERRITIN / ARTIFICIAL METALLOPROTEIN
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(II) allyl complex / Ferritin light chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsAbe, S. / Niemeyer, J. / Abe, M. / Ueno, T. / Hikage, T. / Erker, G. / Watanabe, Y.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: Control of the coordination structure of organometallic palladium complexes in an apo-ferritin cage.
Authors: Abe, S. / Niemeyer, J. / Abe, M. / Takezawa, Y. / Ueno, T. / Hikage, T. / Erker, G. / Watanabe, Y.
History
DepositionJan 18, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _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
X: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,10115
Polymers19,7891
Non-polymers1,31214
Water3,783210
1
X: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)506,421360
Polymers474,94424
Non-polymers31,477336
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 area118020 Å2
ΔGint-1609 kcal/mol
Surface area133540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.176, 181.176, 181.176
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-175-

CD

21X-208-

HOH

31X-291-

HOH

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Components

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Protein , 1 types, 1 molecules X

#1: Protein Ferritin light chain / Ferritin L subunit


Mass: 19789.314 Da / Num. of mol.: 1 / Mutation: H114A
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

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Non-polymers , 5 types, 224 molecules

#2: Chemical ChemComp-CD / CADMIUM ION


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


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PLL / Palladium(II) allyl complex


Mass: 147.492 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5Pd
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsIN THE LIGAND PLL, ALL C-C BOND TYPES ARE DELOCALIZED BONDS AND PD-C BONDS ARE PI BONDS.
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: 3.13 Å3/Da / Density % sol: 60.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulfate, cadmium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jul 3, 2007
RadiationMonochromator: CONFOCAL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 26016 / % possible obs: 99.1 % / Redundancy: 6.7 % / Biso Wilson estimate: 20.186 Å2 / Rmerge(I) obs: 0.061
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.302 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DAT

1dat


Resolution: 1.75→25.13 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.7 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21127 1318 5.1 %RANDOM
Rwork0.17725 ---
obs0.1789 24666 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.411 Å2
Refinement stepCycle: LAST / Resolution: 1.75→25.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1437 0 57 210 1704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221518
X-RAY DIFFRACTIONr_angle_refined_deg1.1812.0242051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0045189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14623.92479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30415275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4351514
X-RAY DIFFRACTIONr_chiral_restr0.090.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021130
X-RAY DIFFRACTIONr_nbd_refined0.2180.2760
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21031
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2167
X-RAY DIFFRACTIONr_metal_ion_refined0.1890.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.293
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.231
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2070.22
X-RAY DIFFRACTIONr_mcbond_it0.8571.5909
X-RAY DIFFRACTIONr_mcangle_it1.30921414
X-RAY DIFFRACTIONr_scbond_it2.3033670
X-RAY DIFFRACTIONr_scangle_it3.6774.5607
X-RAY DIFFRACTIONr_sphericity_free31.70231
X-RAY DIFFRACTIONr_sphericity_bonded5.02333
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 109 -
Rwork0.224 1761 -
obs--98.32 %

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