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- PDB-5gu0: Crystal structure of Au.CL-apo-E45C/R52C-rHLFr -

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Basic information

Entry
Database: PDB / ID: 5gu0
TitleCrystal structure of Au.CL-apo-E45C/R52C-rHLFr
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / IRON STORAGE
Function / homology
Function and homology information


ferritin complex / autolysosome / ferric iron binding / autophagosome / ferrous iron binding / iron ion transport / 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 / Ferritin, core subunit, four-helix bundle / 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 / Ferritin, core subunit, four-helix bundle / 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 / MAD / Resolution: 1.95 Å
AuthorsMaity, B. / Abe, S. / Ueno, T.
CitationJournal: Nat Commun / Year: 2017
Title: Observation of gold sub-nanocluster nucleation within a crystalline protein cage
Authors: Maity, B. / Abe, S. / Ueno, T.
History
DepositionAug 24, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)22,02216
Polymers19,7921
Non-polymers2,22915
Water1,38777
1
X: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)528,519384
Polymers475,01824
Non-polymers53,502360
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 area109870 Å2
ΔGint-1145 kcal/mol
Surface area139220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.892, 180.892, 180.892
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-209-

CD

21X-210-

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: 19792.406 Da / Num. of mol.: 1 / Mutation: E45C,R52C
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 , 5 types, 92 molecules

#2: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 8 / 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.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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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: 3.12 Å3/Da / Density % sol: 60.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulphate, Cadmium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1.03586, 1.05777
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.035861
21.057771
ReflectionResolution: 1.95→40 Å / Num. obs: 19055 / % possible obs: 99.9 % / Redundancy: 11 % / Net I/σ(I): 65.7
Reflection shellRedundancy: 11.3 % / Mean I/σ(I) obs: 12.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOLREPdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.95→31.98 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.49 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.116 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20494 981 5.2 %RANDOM
Rwork0.17734 ---
obs0.17871 18055 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.491 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.95→31.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1341 0 29 77 1447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191390
X-RAY DIFFRACTIONr_bond_other_d0.0030.021328
X-RAY DIFFRACTIONr_angle_refined_deg1.9391.9731874
X-RAY DIFFRACTIONr_angle_other_deg1.06133041
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3025173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5124.28670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.87915245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5831510
X-RAY DIFFRACTIONr_chiral_restr0.1130.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021587
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02333
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_it2.622.588683
X-RAY DIFFRACTIONr_mcbond_other2.5942.583682
X-RAY DIFFRACTIONr_mcangle_it3.6073.858853
X-RAY DIFFRACTIONr_mcangle_other3.6113.862854
X-RAY DIFFRACTIONr_scbond_it4.373.129706
X-RAY DIFFRACTIONr_scbond_other4.223.089693
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5964.4381004
X-RAY DIFFRACTIONr_long_range_B_refined7.75421.3681657
X-RAY DIFFRACTIONr_long_range_B_other7.67221.1711628
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 63 -
Rwork0.211 1323 -
obs--99.93 %

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