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- PDB-7vip: Crystal structure of Au(10EQ)-apo-R168H/L169C-rHLFr -

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Basic information

Entry
Database: PDB / ID: 7vip
TitleCrystal structure of Au(10EQ)-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)20,8559
Polymers19,8431
Non-polymers1,0118
Water3,117173
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)500,515216
Polymers476,24124
Non-polymers24,274192
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 area100520 Å2
ΔGint-502 kcal/mol
Surface area141600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.126, 182.126, 182.126
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-203-

CD

21A-204-

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: 19843.365 Da / Num. of mol.: 1 / Mutation: 168H/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, 181 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CD / CADMIUM ION


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


Mass: 196.967 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Au / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 3.17 Å3/Da / Density % sol: 61.21 %
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→12.882 Å / Num. obs: 20892 / % possible obs: 99.7 % / Redundancy: 9.5 % / CC1/2: 1 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.013 / Net I/σ(I): 50.6
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.145 / Mean I/σ(I) obs: 12.2 / Num. unique obs: 1403 / CC1/2: 0.988 / Rpim(I) all: 0.058 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CrysalisProdata reduction
Cootmodel building
MOLREPphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DAT

1dat


Resolution: 1.9→12.882 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.912 / WRfactor Rfree: 0.187 / WRfactor Rwork: 0.156 / SU B: 2.165 / SU ML: 0.066 / Average fsc free: 0.9488 / Average fsc work: 0.9572 / Cross valid method: FREE R-VALUE / ESU R: 0.12 / ESU R Free: 0.116 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2117 1054 5.05 %
Rwork0.1807 19819 -
all0.182 --
obs-20873 99.443 %
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: 12.442 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→12.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1368 0 22 173 1563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121422
X-RAY DIFFRACTIONr_angle_refined_deg1.8251.6241916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5025175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.27122.73884
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48515251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1671510
X-RAY DIFFRACTIONr_chiral_restr0.1070.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021080
X-RAY DIFFRACTIONr_nbd_refined0.240.2732
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21006
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2131
X-RAY DIFFRACTIONr_metal_ion_refined0.570.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2440.281
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1620.235
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.570.21
X-RAY DIFFRACTIONr_mcbond_it1.5060.948697
X-RAY DIFFRACTIONr_mcangle_it2.4421.405873
X-RAY DIFFRACTIONr_scbond_it2.5771.207724
X-RAY DIFFRACTIONr_scangle_it3.9011.6961042
X-RAY DIFFRACTIONr_lrange_it6.22914.2092304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.245710.1871445X-RAY DIFFRACTION100
1.949-2.0030.248690.2121396X-RAY DIFFRACTION100
2.003-2.0610.178620.1891385X-RAY DIFFRACTION100
2.061-2.1240.214740.1831316X-RAY DIFFRACTION99.9281
2.124-2.1940.202650.1891281X-RAY DIFFRACTION99.9258
2.194-2.2710.178770.1671251X-RAY DIFFRACTION100
2.271-2.3560.163680.1731194X-RAY DIFFRACTION99.9208
2.356-2.4530.151620.1631164X-RAY DIFFRACTION100
2.453-2.5620.197600.1681125X-RAY DIFFRACTION100
2.562-2.6870.213540.1771079X-RAY DIFFRACTION100
2.687-2.8320.258470.1841022X-RAY DIFFRACTION100
2.832-3.0030.214540.186981X-RAY DIFFRACTION100
3.003-3.2110.218450.176929X-RAY DIFFRACTION100
3.211-3.4680.257470.183860X-RAY DIFFRACTION99.8899
3.468-3.7980.212400.162802X-RAY DIFFRACTION100
3.798-4.2460.203440.174723X-RAY DIFFRACTION99.4812
4.246-4.9010.258360.174653X-RAY DIFFRACTION100
4.901-5.9990.233370.208565X-RAY DIFFRACTION100
5.999-8.4710.206300.211455X-RAY DIFFRACTION100
8.471-12.8820.195120.194193X-RAY DIFFRACTION65.2866

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