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- PDB-8h8m: Crystal structure of apo-E53F/E57F/E60F/E64F-rHLFr -

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Basic information

Entry
Database: PDB / ID: 8h8m
TitleCrystal structure of apo-E53F/E57F/E60F/E64F-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)21,07213
Polymers19,9171
Non-polymers1,15512
Water4,197233
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)505,717312
Polymers477,99824
Non-polymers27,719288
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 area94530 Å2
ΔGint-560 kcal/mol
Surface area135460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.108, 181.108, 181.108
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-508-

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: 19916.590 Da / Num. of mol.: 1 / Mutation: E53F,E57F,E60F,E64F
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-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.: 8 / 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.: 233 / 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: 3.11 Å3/Da / Density % sol: 60.41 %
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→20.257 Å / Num. obs: 41145 / % possible obs: 100 % / Redundancy: 12.2 % / CC1/2: 1 / Net I/σ(I): 28.9
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 2008 / CC1/2: 0.896

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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→20.257 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.968 / SU ML: 0.036 / Cross valid method: FREE R-VALUE / ESU R: 0.057 / ESU R Free: 0.057
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1762 2087 5.086 %
Rwork0.1592 38949 -
all0.16 --
obs-41036 99.65 %
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: 12.727 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1378 0 22 233 1633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131549
X-RAY DIFFRACTIONr_bond_other_d0.0020.0151483
X-RAY DIFFRACTIONr_angle_refined_deg1.9071.6362112
X-RAY DIFFRACTIONr_angle_other_deg1.6041.5793414
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7845208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90622.0299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14815283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6481513
X-RAY DIFFRACTIONr_chiral_restr0.0950.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021812
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02402
X-RAY DIFFRACTIONr_nbd_refined0.2490.2338
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1680.21245
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2733
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.2625
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2147
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0460.21
X-RAY DIFFRACTIONr_metal_ion_refined0.4530.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3320.225
X-RAY DIFFRACTIONr_nbd_other0.1770.285
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.170.229
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.4530.22
X-RAY DIFFRACTIONr_mcbond_it1.3531.067725
X-RAY DIFFRACTIONr_mcbond_other1.3141.062724
X-RAY DIFFRACTIONr_mcangle_it2.1081.593914
X-RAY DIFFRACTIONr_mcangle_other2.1111.598915
X-RAY DIFFRACTIONr_scbond_it2.4181.322823
X-RAY DIFFRACTIONr_scbond_other2.3971.315820
X-RAY DIFFRACTIONr_scangle_it3.7521.8881178
X-RAY DIFFRACTIONr_scangle_other3.7531.8751173
X-RAY DIFFRACTIONr_lrange_it5.80114.1771862
X-RAY DIFFRACTIONr_lrange_other5.4913.0071789
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5390.2521570.2112857X-RAY DIFFRACTION99.9668
1.539-1.5810.2091210.2012761X-RAY DIFFRACTION100
1.581-1.6270.2231280.1882708X-RAY DIFFRACTION99.9648
1.627-1.6770.1841510.1792599X-RAY DIFFRACTION100
1.677-1.7320.21450.172531X-RAY DIFFRACTION100
1.732-1.7930.2231480.1632422X-RAY DIFFRACTION99.9222
1.793-1.8610.1931100.1612404X-RAY DIFFRACTION99.9205
1.861-1.9370.241210.162281X-RAY DIFFRACTION100
1.937-2.0230.181290.1632197X-RAY DIFFRACTION99.8283
2.023-2.1220.141220.1432089X-RAY DIFFRACTION99.8194
2.122-2.2360.1651070.1392015X-RAY DIFFRACTION99.6244
2.236-2.3720.1421010.1311899X-RAY DIFFRACTION99.1572
2.372-2.5350.19770.1411789X-RAY DIFFRACTION99.2026
2.535-2.7380.143940.1311679X-RAY DIFFRACTION98.8846
2.738-30.135760.1461566X-RAY DIFFRACTION99.3345
3-3.3530.184780.1521410X-RAY DIFFRACTION99.5984
3.353-3.8710.184740.1581267X-RAY DIFFRACTION99.4807
3.871-4.740.146610.1411094X-RAY DIFFRACTION99.4832
4.74-6.6960.178580.201861X-RAY DIFFRACTION99.4589
6.696-20.2570.176290.226520X-RAY DIFFRACTION94.1681

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