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- PDB-7vit: Crystal structure of Au(400EQ)-apo-R168H/L169C-rHLFr -

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Basic information

Entry
Database: PDB / ID: 7vit
TitleCrystal structure of Au(400EQ)-apo-R168H/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: 1.9 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)22,01916
Polymers19,8431
Non-polymers2,17615
Water4,143230
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)528,465384
Polymers476,24124
Non-polymers52,224360
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 area112180 Å2
ΔGint-1293 kcal/mol
Surface area137130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.889, 180.889, 180.889
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-202-

CD

31A-211-

CD

41A-465-

HOH

51A-516-

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: 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

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Non-polymers , 5 types, 245 molecules

#2: Chemical ChemComp-CD / CADMIUM ION


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


Mass: 196.967 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Au / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 3.1 Å3/Da / Density % sol: 60.29 %
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 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.540562 Å / Relative weight: 1
ReflectionResolution: 1.9→12.957 Å / Num. obs: 20431 / % possible obs: 99.7 % / Redundancy: 10.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.046 / Rrim(I) all: 0.149 / Net I/σ(I): 17.7
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.651 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1364 / CC1/2: 0.874 / Rpim(I) all: 0.249 / Rrim(I) all: 0.698 / % 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→12.957 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.225 / WRfactor Rwork: 0.187 / SU B: 2.675 / SU ML: 0.079 / Average fsc free: 0.9434 / Average fsc work: 0.9511 / Cross valid method: FREE R-VALUE / ESU R: 0.133 / ESU R Free: 0.126
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.217 1038 5.232 %
Rwork0.1831 18802 -
all0.185 --
obs-19840 96.362 %
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: 17.355 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→12.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1362 0 23 230 1615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121445
X-RAY DIFFRACTIONr_angle_refined_deg1.6781.6261954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.285180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3222.15988
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11515260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6561512
X-RAY DIFFRACTIONr_chiral_restr0.1090.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021110
X-RAY DIFFRACTIONr_nbd_refined0.2230.2802
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21009
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2660.2190
X-RAY DIFFRACTIONr_metal_ion_refined0.1330.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.260.295
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2670.256
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2370.21
X-RAY DIFFRACTIONr_mcbond_it1.4321.385708
X-RAY DIFFRACTIONr_mcangle_it2.2392.058892
X-RAY DIFFRACTIONr_scbond_it2.521.649735
X-RAY DIFFRACTIONr_scangle_it3.8152.3811061
X-RAY DIFFRACTIONr_lrange_it6.49221.0272476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.263840.241391X-RAY DIFFRACTION98.3333
1.949-2.0030.308520.2361359X-RAY DIFFRACTION97.8502
2.003-2.0610.23750.2251294X-RAY DIFFRACTION97.9957
2.061-2.1240.255690.221256X-RAY DIFFRACTION96.8567
2.124-2.1940.35670.2091208X-RAY DIFFRACTION95.5056
2.194-2.2710.225660.2071180X-RAY DIFFRACTION96.365
2.271-2.3560.234520.1921124X-RAY DIFFRACTION94.9153
2.356-2.4530.182610.191093X-RAY DIFFRACTION95.136
2.453-2.5620.278520.1871057X-RAY DIFFRACTION96.2674
2.562-2.6870.184570.171999X-RAY DIFFRACTION95.8258
2.687-2.8320.201530.17983X-RAY DIFFRACTION96.8224
2.832-3.0030.273530.166899X-RAY DIFFRACTION95.4865
3.003-3.2110.174540.16876X-RAY DIFFRACTION96.6736
3.211-3.4680.188460.156810X-RAY DIFFRACTION95.9641
3.468-3.7980.219430.149764X-RAY DIFFRACTION98.8971
3.798-4.2460.172400.153695X-RAY DIFFRACTION96.4567
4.246-4.9010.163470.146628X-RAY DIFFRACTION98.6842
4.901-5.9990.199330.181537X-RAY DIFFRACTION98.2759
5.999-8.470.21220.198455X-RAY DIFFRACTION99.7908
8.47-12.9570.266120.232194X-RAY DIFFRACTION67.3203

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