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- PDB-8h8l: Crystal structure of apo-R52F/E56F/R59F/E63F-rHLFr -

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Basic information

Entry
Database: PDB / ID: 8h8l
TitleCrystal structure of apo-R52F/E56F/R59F/E63F-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: 1.5 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)21,20614
Polymers19,8891
Non-polymers1,31813
Water4,342241
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)508,949336
Polymers477,32424
Non-polymers31,625312
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 area92430 Å2
ΔGint-375 kcal/mol
Surface area141800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.310, 181.310, 181.310
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-202-

CD

21A-203-

CD

31A-204-

CD

41A-467-

HOH

51A-520-

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: 19888.508 Da / Num. of mol.: 1 / Mutation: R52F,E56F,R59F,E63F
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, 254 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-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 10 / 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.: 241 / 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: 3.12 Å3/Da / Density % sol: 60.6 %
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→20.279 Å / Num. obs: 41282 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 1 / Net I/σ(I): 30.4
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 2010 / CC1/2: 0.951

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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→20.279 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.152 / WRfactor Rwork: 0.141 / SU B: 0.873 / SU ML: 0.033 / Average fsc free: 0.9628 / Average fsc work: 0.9666 / Cross valid method: FREE R-VALUE / ESU R: 0.056 / ESU R Free: 0.055
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1712 2051 4.979 %
Rwork0.1564 39142 -
all0.157 --
obs-41193 99.724 %
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: 10.481 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1386 0 20 241 1647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131554
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151486
X-RAY DIFFRACTIONr_angle_refined_deg1.8861.6352119
X-RAY DIFFRACTIONr_angle_other_deg1.6171.5813432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7895209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95722.78497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78415290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0121511
X-RAY DIFFRACTIONr_chiral_restr0.0960.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021822
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02392
X-RAY DIFFRACTIONr_nbd_refined0.250.2346
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1580.21232
X-RAY DIFFRACTIONr_nbtor_refined0.1880.2721
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.2634
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2151
X-RAY DIFFRACTIONr_metal_ion_refined0.1110.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3770.214
X-RAY DIFFRACTIONr_nbd_other0.2160.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1680.230
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1480.23
X-RAY DIFFRACTIONr_mcbond_it1.1130.877731
X-RAY DIFFRACTIONr_mcbond_other1.1080.877731
X-RAY DIFFRACTIONr_mcangle_it1.8351.31922
X-RAY DIFFRACTIONr_mcangle_other1.8371.315923
X-RAY DIFFRACTIONr_scbond_it1.8391.05822
X-RAY DIFFRACTIONr_scbond_other1.8051.042819
X-RAY DIFFRACTIONr_scangle_it2.7541.5061178
X-RAY DIFFRACTIONr_scangle_other2.7491.4911173
X-RAY DIFFRACTIONr_lrange_it5.09411.8081873
X-RAY DIFFRACTIONr_lrange_other4.52910.6081791
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5390.2631410.1892848X-RAY DIFFRACTION99.9666
1.539-1.5810.1781520.1822755X-RAY DIFFRACTION100
1.581-1.6270.1751470.172699X-RAY DIFFRACTION99.9649
1.627-1.6770.1641610.1632606X-RAY DIFFRACTION99.9278
1.677-1.7320.1881280.1632564X-RAY DIFFRACTION100
1.732-1.7930.1771270.1572452X-RAY DIFFRACTION99.9612
1.793-1.8610.1671420.1542365X-RAY DIFFRACTION100
1.861-1.9370.1971290.1622276X-RAY DIFFRACTION99.3802
1.937-2.0230.1781140.1612216X-RAY DIFFRACTION99.8286
2.023-2.1220.159880.1442144X-RAY DIFFRACTION99.8658
2.122-2.2360.168970.142010X-RAY DIFFRACTION99.1529
2.236-2.3720.164930.141924X-RAY DIFFRACTION99.7034
2.372-2.5360.203890.1351809X-RAY DIFFRACTION99.7373
2.536-2.7390.148820.1291712X-RAY DIFFRACTION99.8886
2.739-30.129910.1371559X-RAY DIFFRACTION99.8789
3-3.3530.166730.1561428X-RAY DIFFRACTION99.8669
3.353-3.8720.142650.1561283X-RAY DIFFRACTION99.7041
3.872-4.740.183590.1491088X-RAY DIFFRACTION99.0501
4.74-6.6970.201400.224888X-RAY DIFFRACTION99.7849
6.697-20.2790.181330.203516X-RAY DIFFRACTION94.0069

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