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- PDB-8i8q: Crystal structure of horse spleen L-ferritin H114A mutant at -180... -

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Basic information

Entry
Database: PDB / ID: 8i8q
TitleCrystal structure of horse spleen L-ferritin H114A mutant at -180deg Celsius.
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / Ferritin / H114A mutant / X-ray structure
Function / homology
Function and homology information


intracellular ferritin complex / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / 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
AuthorsMaity, B. / Tian, J. / Abe, S. / Ueno, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Cryst.Growth Des. / Year: 2023
Title: Atomic-level insights into a unique semi-clathrate hydrate formed in a confined environment of porous protein crystal.
Authors: Maity, B. / Tian, J. / Furuta, T. / Abe, S. / Ueno, T.
History
DepositionFeb 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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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)21,21416
Polymers19,8051
Non-polymers1,40915
Water4,612256
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)509,148384
Polymers475,32924
Non-polymers33,819360
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
crystal symmetry operation13_554y,x,-z-11
crystal symmetry operation14_554-y,-x,-z-11
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation33_554y,z+1/2,x-1/21
crystal symmetry operation34_554-y,z+1/2,-x-1/21
crystal symmetry operation35_544y,-z-1/2,-x-1/21
crystal symmetry operation36_544-y,-z-1/2,x-1/21
crystal symmetry operation41_554x,z+1/2,-y-1/21
crystal symmetry operation42_554-x,z+1/2,y-1/21
crystal symmetry operation43_544-x,-z-1/2,-y-1/21
crystal symmetry operation44_544x,-z-1/2,y-1/21
crystal symmetry operation53_554z+1/2,x,y-1/21
crystal symmetry operation54_554z+1/2,-x,-y-1/21
crystal symmetry operation55_454-z-1/2,-x,y-1/21
crystal symmetry operation56_454-z-1/2,x,-y-1/21
crystal symmetry operation69_554z+1/2,y,-x-1/21
crystal symmetry operation70_554z+1/2,-y,x-1/21
crystal symmetry operation71_454-z-1/2,y,x-1/21
crystal symmetry operation72_454-z-1/2,-y,-x-1/21
Buried area96590 Å2
ΔGint-640 kcal/mol
Surface area144270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.219, 182.219, 182.219
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-201-

CD

21A-202-

CD

31A-203-

CD

41A-528-

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: 19805.357 Da / Num. of mol.: 1 / Mutation: H114A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: FTL / Plasmid: PMK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P02791

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Non-polymers , 5 types, 271 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 3.18 Å3/Da / Density % sol: 61.35 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Ammonium sulfate (0.5-1.0M), Cadmium sulfate(12-20mM)
Temp details: Non-shaking incubation

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Data collection

DiffractionMean temperature: 93.15 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Aug 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→19.109 Å / Num. obs: 41908 / % possible obs: 100 % / Redundancy: 8.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.068 / Net I/σ(I): 25
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.438 / Num. unique obs: 2024 / CC1/2: 0.918 / Rrim(I) all: 0.478

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Processing

Software
NameVersionClassification
CrysalisProv42data collection
CrysalisProv42data reduction
Aimless0.7.9data scaling
MOLREP11.9.02phasing
REFMAC5.8.0403refinement
Coot0.9.8.6 ELmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→19.1 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.903 / SU ML: 0.034 / Cross valid method: FREE R-VALUE / ESU R: 0.056 / ESU R Free: 0.056
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1741 2109 5.042 %
Rwork0.1593 39717 -
all0.16 --
obs-41826 99.757 %
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: 10.184 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1388 0 36 256 1680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121491
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161414
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.6472016
X-RAY DIFFRACTIONr_angle_other_deg0.611.5773249
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9225189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.511513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05810270
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.7111082
X-RAY DIFFRACTIONr_chiral_restr0.0870.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021792
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02364
X-RAY DIFFRACTIONr_nbd_refined0.2540.2326
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1690.21139
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2722
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.2778
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2168
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1840.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1110.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3250.220
X-RAY DIFFRACTIONr_nbd_other0.1490.281
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1550.240
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1390.23
X-RAY DIFFRACTIONr_mcbond_it1.5660.883711
X-RAY DIFFRACTIONr_mcbond_other1.5540.884711
X-RAY DIFFRACTIONr_mcangle_it2.3171.576891
X-RAY DIFFRACTIONr_mcangle_other2.3161.583892
X-RAY DIFFRACTIONr_scbond_it2.5611.181780
X-RAY DIFFRACTIONr_scbond_other2.5591.183781
X-RAY DIFFRACTIONr_scangle_it4.0192.0241117
X-RAY DIFFRACTIONr_scangle_other4.0172.0261118
X-RAY DIFFRACTIONr_lrange_it5.56413.031844
X-RAY DIFFRACTIONr_lrange_other5.56413.0341845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5390.221510.1832876X-RAY DIFFRACTION100
1.539-1.5810.2131480.1832770X-RAY DIFFRACTION100
1.581-1.6260.1831530.1712714X-RAY DIFFRACTION100
1.626-1.6760.1521270.1612668X-RAY DIFFRACTION100
1.676-1.730.1741460.1642566X-RAY DIFFRACTION100
1.73-1.7910.2011360.162481X-RAY DIFFRACTION100
1.791-1.8580.1651260.1472419X-RAY DIFFRACTION100
1.858-1.9330.1861340.1872295X-RAY DIFFRACTION99.4676
1.933-2.0180.1541210.1582236X-RAY DIFFRACTION99.9576
2.018-2.1150.1621020.1372158X-RAY DIFFRACTION99.9558
2.115-2.2280.1641060.1442042X-RAY DIFFRACTION99.2148
2.228-2.3610.1641110.1511901X-RAY DIFFRACTION98.967
2.361-2.5210.173970.1321836X-RAY DIFFRACTION100
2.521-2.7190.162880.141735X-RAY DIFFRACTION100
2.719-2.9730.175890.1461580X-RAY DIFFRACTION100
2.973-3.3140.153770.1571470X-RAY DIFFRACTION100
3.314-3.8070.156720.1611299X-RAY DIFFRACTION99.4199
3.807-4.6170.189490.1541134X-RAY DIFFRACTION99.9155
4.617-6.3470.216440.202921X-RAY DIFFRACTION100
6.347-19.10.18320.212616X-RAY DIFFRACTION99.8459

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