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- PDB-7vis: Crystal structure of Au(200EQ)-apo-R168H/L169C-rHLFr -

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Basic information

Entry
Database: PDB / ID: 7vis
TitleCrystal structure of Au(200EQ)-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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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)21,78815
Polymers19,8431
Non-polymers1,94514
Water2,990166
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)522,922360
Polymers476,24124
Non-polymers46,681336
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_565z,-y+1,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_565-z,-y+1,-x1
crystal symmetry operation29_554z,x+1/2,y-1/21
crystal symmetry operation30_555z,-x+1/2,-y+1/21
crystal symmetry operation31_554-z,-x+1/2,y-1/21
crystal symmetry operation32_555-z,x+1/2,-y+1/21
crystal symmetry operation41_555x,z+1/2,-y+1/21
crystal symmetry operation42_554-x,z+1/2,y-1/21
crystal symmetry operation43_555-x,-z+1/2,-y+1/21
crystal symmetry operation44_554x,-z+1/2,y-1/21
crystal symmetry operation81_455y-1/2,z+1/2,x1
crystal symmetry operation82_555-y+1/2,z+1/2,-x1
crystal symmetry operation83_455y-1/2,-z+1/2,-x1
crystal symmetry operation84_555-y+1/2,-z+1/2,x1
crystal symmetry operation85_455y-1/2,x+1/2,-z1
crystal symmetry operation86_555-y+1/2,-x+1/2,-z1
crystal symmetry operation87_455y-1/2,-x+1/2,z1
crystal symmetry operation88_555-y+1/2,x+1/2,z1
Buried area103060 Å2
ΔGint-486 kcal/mol
Surface area139370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.594, 182.594, 182.594
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-209-

CD

21A-210-

CD

31A-211-

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: 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 , 6 types, 180 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Au / Feature type: SUBJECT OF INVESTIGATION
#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.: 1 / Source method: isolated from a natural source / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 3.19 Å3/Da / Density % sol: 61.49 %
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: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→45.69 Å / Num. obs: 22847 / % possible obs: 100 % / Redundancy: 1.8 % / CC1/2: 0.856 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.07 / Rrim(I) all: 0.099 / Net I/σ(I): 9.1
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.075 / Num. unique obs: 1375 / CC1/2: 0.978 / Rpim(I) all: 0.075 / Rrim(I) all: 0.106

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1dat

1dat


Resolution: 1.85→45.69 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.231 / WRfactor Rwork: 0.188 / SU B: 1.874 / SU ML: 0.058 / Average fsc free: 0.953 / Average fsc work: 0.9611 / Cross valid method: FREE R-VALUE / ESU R: 0.099 / ESU R Free: 0.1
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.198 1116 4.89 %
Rwork0.1662 21707 -
all0.168 --
obs-22823 99.886 %
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: 13.278 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.85→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1363 0 21 166 1550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121399
X-RAY DIFFRACTIONr_angle_refined_deg1.7881.6251885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2725172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.94422.65183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51815250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.881510
X-RAY DIFFRACTIONr_chiral_restr0.1070.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021060
X-RAY DIFFRACTIONr_nbd_refined0.2220.2656
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2972
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2112
X-RAY DIFFRACTIONr_metal_ion_refined0.2530.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2740.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1150.233
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.3420.23
X-RAY DIFFRACTIONr_mcbond_it1.2950.996685
X-RAY DIFFRACTIONr_mcangle_it1.8151.481855
X-RAY DIFFRACTIONr_scbond_it2.7881.329713
X-RAY DIFFRACTIONr_scangle_it4.3511.8651029
X-RAY DIFFRACTIONr_lrange_it5.76515.0912191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8980.219850.191563X-RAY DIFFRACTION99.9394
1.898-1.950.179710.1811530X-RAY DIFFRACTION99.7508
1.95-2.0070.219820.1711466X-RAY DIFFRACTION99.871
2.007-2.0680.179660.1711468X-RAY DIFFRACTION99.9349
2.068-2.1360.217630.1631406X-RAY DIFFRACTION100
2.136-2.2110.191840.1661339X-RAY DIFFRACTION99.9298
2.211-2.2940.199750.1581321X-RAY DIFFRACTION100
2.294-2.3880.194690.1611266X-RAY DIFFRACTION99.9251
2.388-2.4940.226560.1611229X-RAY DIFFRACTION99.9222
2.494-2.6160.226540.161176X-RAY DIFFRACTION100
2.616-2.7570.175570.1411129X-RAY DIFFRACTION100
2.757-2.9240.173540.1471055X-RAY DIFFRACTION100
2.924-3.1260.185560.163999X-RAY DIFFRACTION99.9053
3.126-3.3760.205440.16943X-RAY DIFFRACTION100
3.376-3.6980.149490.155873X-RAY DIFFRACTION99.8917
3.698-4.1340.169440.155798X-RAY DIFFRACTION99.8814
4.134-4.7720.202370.152714X-RAY DIFFRACTION100
4.772-5.8420.215340.189613X-RAY DIFFRACTION99.5385
5.842-8.2490.293220.244503X-RAY DIFFRACTION99.6205
8.249-45.690.275140.21316X-RAY DIFFRACTION97.9229

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