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- PDB-8h8o: Crystal structure of apo-R52W/E56W/R59W/E63W-rHLFr -

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Basic information

Entry
Database: PDB / ID: 8h8o
TitleCrystal structure of apo-R52W/E56W/R59W/E63W-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 / 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: 1.5 Å
AuthorsHishikawa, Y. / Noya, H. / Maity, B. / Abe, S. / Ueno, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Chemistry / Year: 2023
Title: Elucidating Conformational Dynamics and Thermostability of Designed Aromatic Clusters by Using Protein Cages.
Authors: Hishikawa, Y. / Noya, H. / Nagatoishi, S. / Yoshidome, T. / Maity, B. / Tsumoto, K. / Abe, S. / Ueno, T.
History
DepositionOct 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,08712
Polymers20,0451
Non-polymers1,04311
Water4,324240
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)506,092288
Polymers481,07224
Non-polymers25,021264
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 area108970 Å2
ΔGint-576 kcal/mol
Surface area138550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.133, 181.133, 181.133
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-204-

CD

21A-205-

CD

31A-206-

CD

41A-458-

HOH

51A-491-

HOH

61A-514-

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: 20044.652 Da / Num. of mol.: 1 / Mutation: R52W,E56W,R59W,E63W
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, 251 molecules

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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.09 Å3/Da / Density % sol: 60.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulphate, Cadmium sulphate

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Mar 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→20.259 Å / Num. obs: 41179 / % possible obs: 100 % / Redundancy: 11.8 % / CC1/2: 1 / Net I/σ(I): 25.1
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 2010 / CC1/2: 0.947

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Processing

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

1dat


Resolution: 1.5→20.259 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.94 / SU ML: 0.035 / Cross valid method: FREE R-VALUE / ESU R: 0.059 / ESU R Free: 0.058
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1788 2068 5.065 %
Rwork0.1619 38759 -
all0.163 --
obs-40827 99.056 %
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: 11.328 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20.259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1393 0 21 240 1654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131567
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151484
X-RAY DIFFRACTIONr_angle_refined_deg1.8581.6292144
X-RAY DIFFRACTIONr_angle_other_deg1.6111.5773422
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6825209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.38622.63295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2715284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1721511
X-RAY DIFFRACTIONr_chiral_restr0.1010.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021823
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02395
X-RAY DIFFRACTIONr_nbd_refined0.2470.2353
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1610.21248
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2725
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.2680
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2149
X-RAY DIFFRACTIONr_metal_ion_refined0.0970.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2540.216
X-RAY DIFFRACTIONr_nbd_other0.1870.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.232
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1370.21
X-RAY DIFFRACTIONr_mcbond_it1.170.95730
X-RAY DIFFRACTIONr_mcbond_other1.1710.95730
X-RAY DIFFRACTIONr_mcangle_it1.8881.414920
X-RAY DIFFRACTIONr_mcangle_other1.8871.419921
X-RAY DIFFRACTIONr_scbond_it2.2931.215836
X-RAY DIFFRACTIONr_scbond_other2.281.21833
X-RAY DIFFRACTIONr_scangle_it3.5051.7431205
X-RAY DIFFRACTIONr_scangle_other3.5111.7311200
X-RAY DIFFRACTIONr_lrange_it5.43312.9921940
X-RAY DIFFRACTIONr_lrange_other5.08811.9151860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5390.231510.2072816X-RAY DIFFRACTION99.7646
1.539-1.5810.2311270.1922814X-RAY DIFFRACTION99.966
1.581-1.6270.2051260.1842681X-RAY DIFFRACTION99.9288
1.627-1.6770.1681490.1742598X-RAY DIFFRACTION99.9272
1.677-1.7320.1871460.1712532X-RAY DIFFRACTION99.8509
1.732-1.7930.2061480.1682438X-RAY DIFFRACTION99.9227
1.793-1.8610.191110.1682385X-RAY DIFFRACTION99.84
1.861-1.9360.1931180.1682260X-RAY DIFFRACTION98.7542
1.936-2.0230.2031260.172167X-RAY DIFFRACTION98.8362
2.023-2.1210.1321220.1492091X-RAY DIFFRACTION99.0157
2.121-2.2360.1621060.1491991X-RAY DIFFRACTION98.2201
2.236-2.3720.154990.1451874X-RAY DIFFRACTION98.0129
2.372-2.5350.189780.1391782X-RAY DIFFRACTION98.4127
2.535-2.7380.152930.1391660X-RAY DIFFRACTION98.1523
2.738-2.9990.126740.1391557X-RAY DIFFRACTION98.253
2.999-3.3530.172760.1541391X-RAY DIFFRACTION98.1928
3.353-3.8710.177700.1551262X-RAY DIFFRACTION98.8131
3.871-4.7390.178600.1471075X-RAY DIFFRACTION98.2684
4.739-6.6960.231590.202864X-RAY DIFFRACTION99.2473
6.696-20.2590.202290.226521X-RAY DIFFRACTION94.3396

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