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- PDB-7vir: Crystal structure of Au(100EQ)-apo-R168H/L169C-rHLFr -

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Basic information

Entry
Database: PDB / ID: 7vir
TitleCrystal structure of Au(100EQ)-apo-R168H/L169C-rHLFr
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / ferritin
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 / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / : / Ferritin light chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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)22,15716
Polymers19,8431
Non-polymers2,31415
Water2,360131
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)531,766384
Polymers476,24124
Non-polymers55,526360
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_545z,-y-1,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_545-z,-y-1,-x1
crystal symmetry operation29_545z,x-1/2,y+1/21
crystal symmetry operation30_544z,-x-1/2,-y-1/21
crystal symmetry operation31_545-z,-x-1/2,y+1/21
crystal symmetry operation32_544-z,x-1/2,-y-1/21
crystal symmetry operation41_544x,z-1/2,-y-1/21
crystal symmetry operation42_545-x,z-1/2,y+1/21
crystal symmetry operation43_544-x,-z-1/2,-y-1/21
crystal symmetry operation44_545x,-z-1/2,y+1/21
crystal symmetry operation81_545y+1/2,z-1/2,x1
crystal symmetry operation82_445-y-1/2,z-1/2,-x1
crystal symmetry operation83_545y+1/2,-z-1/2,-x1
crystal symmetry operation84_445-y-1/2,-z-1/2,x1
crystal symmetry operation85_545y+1/2,x-1/2,-z1
crystal symmetry operation86_445-y-1/2,-x-1/2,-z1
crystal symmetry operation87_545y+1/2,-x-1/2,z1
crystal symmetry operation88_445-y-1/2,x-1/2,z1
Buried area117240 Å2
ΔGint-1281 kcal/mol
Surface area131490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.213, 180.213, 180.213
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-201-

CD

21A-203-

CD

31A-214-

CD

41A-215-

SO4

51A-430-

HOH

61A-431-

HOH

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Components

#1: Protein Ferritin light chain / Ferritin L subunit


Mass: 19843.365 Da / Num. of mol.: 1 / Mutation: R168H/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
#2: Chemical
ChemComp-CD / CADMIUM ION


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


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Au / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
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: 3.07 Å3/Da / Density % sol: 59.94 %
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: Feb 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.540562 Å / Relative weight: 1
ReflectionResolution: 1.9→12.91 Å / Num. obs: 20252 / % possible obs: 99.7 % / Redundancy: 9.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.03 / Rrim(I) all: 0.096 / Net I/σ(I): 21.5
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1322 / CC1/2: 0.877 / Rpim(I) all: 0.237 / Rrim(I) all: 0.606 / % possible all: 100

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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: 1.9→12.909 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.178 / WRfactor Rwork: 0.143 / SU B: 2.274 / SU ML: 0.068 / Average fsc free: 0.9498 / Average fsc work: 0.9582 / Cross valid method: FREE R-VALUE / ESU R: 0.114 / ESU R Free: 0.115
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2085 991 4.894 %
Rwork0.17 19259 -
all0.172 --
obs-20250 99.489 %
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: 16.605 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→12.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1363 0 27 131 1521
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121438
X-RAY DIFFRACTIONr_angle_refined_deg1.7751.6241948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2125182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.58822.52987
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54615259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4411511
X-RAY DIFFRACTIONr_chiral_restr0.1060.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021097
X-RAY DIFFRACTIONr_nbd_refined0.2270.2682
X-RAY DIFFRACTIONr_nbtor_refined0.3110.2981
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2101
X-RAY DIFFRACTIONr_metal_ion_refined0.0950.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2320.287
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1790.241
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0950.21
X-RAY DIFFRACTIONr_mcbond_it1.6021.365698
X-RAY DIFFRACTIONr_mcangle_it2.3152.031875
X-RAY DIFFRACTIONr_scbond_it2.9751.687738
X-RAY DIFFRACTIONr_scangle_it4.4542.4061067
X-RAY DIFFRACTIONr_lrange_it6.11719.552227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.256700.2211400X-RAY DIFFRACTION100
1.949-2.0030.181620.2051362X-RAY DIFFRACTION99.9298
2.003-2.0610.249620.1791332X-RAY DIFFRACTION100
2.061-2.1240.184690.1731295X-RAY DIFFRACTION100
2.124-2.1940.226720.1741221X-RAY DIFFRACTION100
2.194-2.2710.223580.1721221X-RAY DIFFRACTION100
2.271-2.3560.205640.1751175X-RAY DIFFRACTION100
2.356-2.4530.184660.1631127X-RAY DIFFRACTION100
2.453-2.5620.205660.1681071X-RAY DIFFRACTION100
2.562-2.6870.233530.1611039X-RAY DIFFRACTION100
2.687-2.8320.186460.1551021X-RAY DIFFRACTION99.9064
2.832-3.0030.208500.153934X-RAY DIFFRACTION100
3.003-3.2110.196440.148898X-RAY DIFFRACTION100
3.211-3.4680.168360.158840X-RAY DIFFRACTION100
3.468-3.7980.184360.152788X-RAY DIFFRACTION100
3.798-4.2460.228350.163717X-RAY DIFFRACTION100
4.246-4.9010.198340.165635X-RAY DIFFRACTION100
4.901-5.9990.234290.215547X-RAY DIFFRACTION100
5.999-8.470.188320.198441X-RAY DIFFRACTION100
8.47-12.9090.51470.16195X-RAY DIFFRACTION66.6667

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