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- PDB-7viu: Crystal structure of Au(200EQ)-apo-R168C/L169C-rHLFr -

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Basic information

Entry
Database: PDB / ID: 7viu
TitleCrystal structure of Au(200EQ)-apo-R168C/L169C-rHLFr
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / ferritin
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 / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLu, C. / Peng, X. / Maity, B. / Ito, N. / Abe, S. / Ueno, T. / Lu, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21878175 China
CitationJournal: Commun Chem / Year: 2022
Title: Design of a gold clustering site in an engineered apo-ferritin cage.
Authors: Lu, C. / Maity, B. / Peng, X. / Ito, N. / Abe, S. / Sheng, X. / Ueno, T. / Lu, D.
History
DepositionSep 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Derived calculations / Category: atom_type / citation
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 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)22,38821
Polymers19,8081
Non-polymers2,58020
Water3,549197
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)537,317504
Polymers475,40124
Non-polymers61,916480
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
crystal symmetry operation13_554y,x,-z-11
crystal symmetry operation14_554-y,-x,-z-11
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation33_554y,z+1/2,x-1/21
crystal symmetry operation34_554-y,z+1/2,-x-1/21
crystal symmetry operation35_544y,-z-1/2,-x-1/21
crystal symmetry operation36_544-y,-z-1/2,x-1/21
crystal symmetry operation41_554x,z+1/2,-y-1/21
crystal symmetry operation42_554-x,z+1/2,y-1/21
crystal symmetry operation43_544-x,-z-1/2,-y-1/21
crystal symmetry operation44_544x,-z-1/2,y-1/21
crystal symmetry operation53_554z+1/2,x,y-1/21
crystal symmetry operation54_554z+1/2,-x,-y-1/21
crystal symmetry operation55_454-z-1/2,-x,y-1/21
crystal symmetry operation56_454-z-1/2,x,-y-1/21
crystal symmetry operation69_554z+1/2,y,-x-1/21
crystal symmetry operation70_554z+1/2,-y,x-1/21
crystal symmetry operation71_454-z-1/2,y,x-1/21
crystal symmetry operation72_454-z-1/2,-y,-x-1/21
Buried area114670 Å2
ΔGint-1035 kcal/mol
Surface area136320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.786, 180.786, 180.786
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-207-

CD

21A-208-

CD

31A-218-

CD

41A-486-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ferritin light chain / Ferritin L subunit


Mass: 19808.361 Da / Num. of mol.: 1 / Mutation: R168C/L169C
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 , 6 types, 217 molecules

#2: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Au / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CD / CADMIUM ION


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


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


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


Mass: 18.015 Da / Num. of mol.: 197 / 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: 3.11 Å3/Da / Density % sol: 60.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: Ammonium Sulfate, Cadmium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.540562 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Aug 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.540562 Å / Relative weight: 1
ReflectionResolution: 1.5→12.95 Å / Num. obs: 40835 / % possible obs: 99.7 % / Redundancy: 9.8 % / CC1/2: 0.999 / Net I/σ(I): 24.2
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 1955 / CC1/2: 0.943

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CrysalisPro171.40_64.67adata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1dat

1dat


Resolution: 1.5→12.95 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.154 / WRfactor Rwork: 0.141 / SU B: 0.852 / SU ML: 0.032 / Average fsc free: 0.9646 / Average fsc work: 0.9683 / Cross valid method: FREE R-VALUE / ESU R: 0.052 / ESU R Free: 0.053 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1668 2069 5.067 %
Rwork0.1513 38763 -
all0.152 --
obs-40832 99.612 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 13.431 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→12.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1372 0 48 197 1617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121464
X-RAY DIFFRACTIONr_angle_refined_deg1.9621.6271972
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1615181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32122.72788
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34115265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3411511
X-RAY DIFFRACTIONr_chiral_restr0.1060.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021103
X-RAY DIFFRACTIONr_nbd_refined0.230.2756
X-RAY DIFFRACTIONr_nbtor_refined0.3160.21007
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2145
X-RAY DIFFRACTIONr_metal_ion_refined0.0810.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2870.284
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1590.233
X-RAY DIFFRACTIONr_mcbond_it1.2460.975703
X-RAY DIFFRACTIONr_mcangle_it1.9761.451882
X-RAY DIFFRACTIONr_scbond_it2.8941.305759
X-RAY DIFFRACTIONr_scangle_it4.1161.8291085
X-RAY DIFFRACTIONr_lrange_it5.84115.5452374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5390.2331500.1822782X-RAY DIFFRACTION98.3563
1.539-1.5810.1991280.1652773X-RAY DIFFRACTION100
1.581-1.6270.1591500.1552650X-RAY DIFFRACTION100
1.627-1.6770.1611330.1512614X-RAY DIFFRACTION100
1.677-1.7320.1731330.1462536X-RAY DIFFRACTION100
1.732-1.7930.1751260.1512432X-RAY DIFFRACTION100
1.793-1.8610.1841200.1472385X-RAY DIFFRACTION100
1.861-1.9370.1611160.1512282X-RAY DIFFRACTION100
1.937-2.0230.1661030.152200X-RAY DIFFRACTION100
2.023-2.1210.1781200.1482092X-RAY DIFFRACTION100
2.121-2.2360.1881140.1422008X-RAY DIFFRACTION100
2.236-2.3720.17950.1441908X-RAY DIFFRACTION100
2.372-2.5350.163970.1441791X-RAY DIFFRACTION99.9471
2.535-2.7380.164940.151678X-RAY DIFFRACTION100
2.738-2.9990.164860.151558X-RAY DIFFRACTION99.9392
2.999-3.3530.145840.1461405X-RAY DIFFRACTION99.7321
3.353-3.8710.135730.1391268X-RAY DIFFRACTION100
3.871-4.740.147680.1471082X-RAY DIFFRACTION99.9131
4.74-6.6960.17570.182867X-RAY DIFFRACTION100
6.696-12.950.186220.175452X-RAY DIFFRACTION82.2917

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