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- PDB-3h7g: Apo-FR with AU ions -

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Basic information

Entry
Database: PDB / ID: 3h7g
TitleApo-FR with AU ions
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / IRON STORAGE / LIGHT CHAIN APOFERRITIN / Iron
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
GOLD 3+ ION / : / Ferritin light chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsAbe, M. / Ueno, T. / Abe, S. / Suzuki, M. / Goto, T. / Toda, Y. / Akita, T. / Yamada, Y. / Watanabe, Y.
CitationJournal: Chem.Commun.(Camb.) / Year: 2009
Title: Preparation and catalytic reaction of Au/Pd bimetallic nanoparticles in apo-ferritin
Authors: Suzuki, M. / Abe, M. / Ueno, T. / Abe, S. / Goto, T. / Toda, Y. / Akita, T. / Yamada, Y. / Watanabe, Y.
History
DepositionApr 27, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)22,03217
Polymers19,8561
Non-polymers2,17616
Water3,189177
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)528,768408
Polymers476,55324
Non-polymers52,214384
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 area103850 Å2
ΔGint-999 kcal/mol
Surface area142320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.632, 181.632, 181.632
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-207-

CD

21A-208-

CD

31A-209-

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: 19856.385 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Plasmid: PMK2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): NOVA BLUE / References: UniProt: P02791

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Non-polymers , 5 types, 193 molecules

#2: Chemical
ChemComp-AU3 / GOLD 3+ ION


Mass: 196.967 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Au
#3: Chemical ChemComp-CD / CADMIUM ION


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


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsREFER TO THE DATABASE, P02791, REF. 2 FOR THIS CONFLICT. THIS SEQUENCE IS FROM BAA03396 IN GENBANK DATABASE.

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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: 3.14 Å3/Da / Density % sol: 60.87 %
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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL38B111.0395
SYNCHROTRONSPring-8 BL38B121.0578
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDMar 8, 2007
ADSC QUANTUM 3152CCDMar 8, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI 111 CHANNELSINGLE WAVELENGTHMx-ray1
2SI 111 CHANNELSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.03951
21.05781
ReflectionResolution: 1.65→35 Å / Num. obs: 31508 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 20.2 % / Biso Wilson estimate: 16.79 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 67.8
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 14 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 8.01 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0005refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DAT

1dat


Resolution: 1.65→30.28 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.912 / SU B: 1.25 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1590 5.1 %RANDOM
Rwork0.209 ---
obs0.21 29893 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.11 Å2
Refinement stepCycle: LAST / Resolution: 1.65→30.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1390 0 48 177 1615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0211480
X-RAY DIFFRACTIONr_angle_refined_deg1.1051.9851991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7975180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5823.79779
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55715269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4241514
X-RAY DIFFRACTIONr_chiral_restr0.0770.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021112
X-RAY DIFFRACTIONr_nbd_refined0.210.2736
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21032
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0980.2116
X-RAY DIFFRACTIONr_metal_ion_refined0.1670.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.220
X-RAY DIFFRACTIONr_mcbond_it0.7941.5887
X-RAY DIFFRACTIONr_mcangle_it1.28921384
X-RAY DIFFRACTIONr_scbond_it2.1943646
X-RAY DIFFRACTIONr_scangle_it3.4494.5603
X-RAY DIFFRACTIONr_sphericity_free11.93639
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 111 -
Rwork0.241 2178 -
obs--99.96 %

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